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The main focus of this review is to discuss the current status of the use of GWAS for fodder quality and biofuel owing to its similarity of traits. Sorghum is a potential multipurpose crop, popularly cultivated for various uses as food, feed fodder, and biomass for ethanol. Production of a huge quantity of biomass and genetic variation for complex sugars are the main motivations not only to use sorghum as fodder for livestock nutritionists but also as a potential candidate for biofuel generation. Few studies have been reported on the knowledge transfer that can be used from the development of biofuel technologies to complement improved fodder quality and vice versa. With recent advances in genotyping technologies, GWAS became one of the primary tools used to identify the genes/genomic regions associated with the phenotype. These modern tools and technologies accelerate the genomic assisted breeding process to enhance the rate of genetic gains. Hence, this mini-review focuses on GWAS studies on genetic architecture and dissection of traits underpinning fodder quality and biofuel traits and their limited comparison with other related model crop species.

Background: Production of biofuels from lignocellulosic crop biomass is an alternative to reduce greenhouse gas emissions. The biofuel production involves collecting biomass, breaking down cell wall components followed by the conversion of sugars to ethanol. The lingo-cellulosic biomass comprises 40-50% cellulose, 20-30% hemicellulose, and 10-25% lignin. Sorghum is a widely adapted energy crop for biofuel production. Biomass with low lignin, high cellulose, and high hemicellulose contents are exploited to attain maximum biofuel production efficiency. Resistance to lodging, pest, disease, and abiotic stresses related to cell wall components is well documented, and quantitative trait loci were identified to understand these traits' genetic correlation. Selection for reduced lignin and increased cellulose content in stover can increase the ethanol yield. The Genome-Wide Association Studies (GWAS) is a complementary approach to evaluating the marker and phenotype associations among large diversity panels. Single nucleotide polymorphisms were scanned to identify loci associated with the traits of interest. In this study, the GWAS was performed on 245 sorghum minicore genotypes to analyze agronomic traits (days to 500lowering, fresh biomass yield, dry biomass yield) and cell wall components (cellulose, hemicellulose, and lignin). Further, in-silico validation of the candidate genes was performed in a global gene expression data from large-scale RNA sequencing studies in sorghum available in the NCBI GEO database was used. Objective: The objectives of this study are to evaluate native variations in biofuel related agronomic traits and stalk cell wall components and to identify significant SNPs or loci related to the cell wall components. Methods: In this article, an association mapping panel, comprising of 245 sorghum minicore germplasm accessions, was evaluated during two post rainy seasons of 2013 and 2014, and observations were recorded on the whole plot- for days to 50% flowering, fresh biomass yield (tha-1), and dry biomass yield (tha-1). The biomass of sun-dried plants from both seasons was collected separately, chopped, dried, and ground to powder. The cellulose, hemicellulose, and lignin contents were determined in the powdered. The content of each of these three components in sorghum was expressed in percent of dry matter. The data on agronomic traits and composition analysis was subjected to Analysis of Variance. For the current study, we remapped the raw GBS data with the sorghum assembly version v3.1. A total of 27,589 SNPs were obtained with a minor allele frequency (MAF)>1% and missing data Results: High broad-sense heritability was exhibited for all the traits in individual seasons along with significant genotype × environment interaction across seasons except lignin. Association mapping with a P-4 revealed genomic regions associated with the- (i) agronomic traits (days to 50% flowering, fresh and dry biomass), and (ii) biochemical traits (cellulose, hemicellulose, and lignin) associated with biofuels production, in individual seasons. Twelve significant SNPs for flowering time, 30 fresh biomass yields, and 24 for dry biomass yield, 25 for cellulose, 7 for hemicellulose, and 21 for lignin were identified. CIRCOS plot was constructed to identify and analyze similarities and differences while comparing the sorghum genome with different crops. For cellulose high similarity of >80% was observed for all sorghum gene sequences with the maize homologs. The overall similarity of sorghum homologs with foxtail millet was >65%, for Arabidopsis from 30.6% to 48.6%, and rice from 28.2% to 92.8%. SNPs for hemicellulose displayed maximum similarity to foxtail millet followed by maize. The sequence similarity of lignin SNPs in sorghum was highest with the maize genome followed by Arabidopsis. Both rice and foxtail millet showed >55% similarity to the sorghum genome. Conclusion: This study reports large variability for agronomic and biofuel traits in the sorghum minicore collection with high heritability. The genetic architecture of cell wall components using the GWAS approach was studied and candidate genes for each component were annotated. These results give a better understanding of the genetic basis of the sorghum cell wall composition. The association analysis identified regions of the genome that could be targeted to enhance the quality of biomass and yield along with the desired composition promoting breeding efficiency for enhanced biofuel yield.

Anthracnose is a prevalent disease of mungbean in Asian countries and Sub-Saharan Africa. It is caused by multiple Colletotrichum species. The high levels of anthracnose resistance in mungbean have not been studied in depth in India, but genetic resistance is desired. In this study, we identified the causal agent of mungbean anthracnose in two regions of India as Colletotrichum truncatum through morphological and molecular methods. A set of 296 mungbean mini-core accessions developed by WorldVeg was screened under a natural disease pressure from July to September (kharif season) in 2016, 2017, and 2018 in Hyderabad (a hot spot for anthracnose) to identify anthracnose resistance. Based on disease severity scores, 22 accessions were consistently anthracnose resistant under the categories of immune, highly resistant, and resistant with scores ranging from ≥1.0 to ≤3.0 during the period of study. Furthermore, based on the agronomic performance, anthracnose resistance in Hyderabad, and other desirable traits, a subset of 74 mungbean accessions was selected from 296 mini-core accessions. These accessions were evaluated under natural disease pressure from July to September in 2018 and 2019 in Palampur (another hot spot for anthracnose) to determine the variation in anthracnose resistance. Out of the 74 accessions, two accessions were resistant in 2018; in 2019, one was immune, nine were highly resistant, and 15 were resistant. Combined analysis of variance of 65 accessions common in Hyderabad and Palampur revealed highly significant effects of environment, genotype (accessions), and genotype × environment interaction on the disease severity. The combined GGE biplot analysis of data across years and locations confirmed that the seven accessions MC-24, MC-51, MC-75, MC-127, MC-207, MC-208, and MC-292 were resistant during 2016 to 2018 in Hyderabad, and only in 2019 in Palampur, and the same accessions were moderately resistant in 2018 in Palampur. The seven resistant accessions identified from both test locations could be used as potential donors in the anthracnose resistance breeding program. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Pearl millet [Pennisetum glaucum (L.) R. Br.] is one of the world’s hardiest warmseason cereal crop cultivated for food and animal feed in the semi-arid tropics of Asia and Africa. This crop faces terminal drought during rainy and flowering-stage heat stress during summer seasons. Blast is emerging as a serious threat affecting its production and productivity in India. Using wild P. violaceum (Lam) Rich. and pearl millet cultivars, prebreeding populations were developed following backcross method. These populations were evaluated in target ecologies in India at three locations during the 2018 summer season for flowering-stage heat stress and at two locations during the 2018 rainy season for terminal drought stress.Atotal 18 introgression lines (ILs) from Population (Pop) 3 exhibited improved seed set under high heat stress vs. the cultivated parent, whereas no IL was better than the cultivated parent in Pop 4. Under rainfed conditions at Hisar and Bawal, India, 19 ILs from Pop 3 and 16 ILs from Pop 4 showed significantly higher dry fodder yield than the cultivated parents. Further, screening of ILs for five diverse pathotype isolates—Pg 45, Pg 138, Pg 186, Pg 204, and Pg 232—of blast resulted in the identification of resistant ILs. Use of these promising ILs in breeding programs will assist in developing new varieties and hybrids with improved tolerance to biotic and abiotic stresses. The study indicated the genetic differences between the parents involved in crossing and also highlighted the importance of precise phenotyping of wild species for target trait prior to use in prebreeding work.

The genome sequences of 16 Streptomyces strains, showing potential for plant growth-promotion (PGP) activities in rice, sorghum, chickpea and pigeonpea, isolated from herbal vermicompost, have been decoded. The genome assemblies of the 16 Streptomyces strains ranged from 6.8 Mb to 8.31 Mb, with a GC content of 72 to 73%. The extent of sequence similarity (in terms of shared ortholog) in 16 Streptomyces strains showed 70 to 85% common genes to the closest publicly available Streptomyces genomes. It was possible to identify ~1,850 molecular functions across these 16 strains, of which close to 50% were conserved across the genomes of Streptomyces strains, whereas, ~10% were strain specific and the rest were present in various combinations. Genome assemblies of the 16 Streptomyces strains have also provided genes involved in key pathways related to PGP and biocontrol traits such as siderophores, auxin, hydrocyanic acid, chitinase and cellulase. Further, the genome assemblies provided better understanding of genetic similarity among target strains and with the publically available Streptomyces strains.

The present investigation aimed to study genetic divergence and clustering pattern of 37super-early pigeon pea genotypes. Analysis of variance and hierarchical cluster analysis of tocher’s method revealed significant differences among the genotypes for all the traits under study. Based on genetic distance (D2 value), the 37 genotypes were grouped into 9 distinctive clusters, of which cluster I and II formed the largest clusters with 10 genotypes in each. Among all the characters understudy, leaf area index(LAI) at 60 DAS contributed more to the divergence followed by leaf area (17.02) and leaf area index (12.71) at maturity. Based on the average inter-cluster distance, the cluster III and IX (66.93) tailed by cluster III and VIII (64.86) and cluster VI and VIII (64.06) showed higher inter-cluster distance depicting the wider divergence. Trait-wise selection of diverse parents from the above clusters aids in exploitation of heterosis in superearly pigeon pea.

Groundnut rust caused by Puccinia arachidis Speg. is a major cause of yield and quality losses in groundnut (Arachis hypogaea L.) in the warm-humid tropics including Tanzania. Breeding and deployment of rust resistant cultivars with farmer-preferred attributes will bolster groundnut production and productivity. The objective of this study was to determine the combining ability effects and gene action controlling rust resistance in groundnut genotypes for breeding. Twelve selected and complementary parental lines were crossed in a diallel design, to develop F1 progenies, which were advanced to the F2 for individual plant selection. Thirty-three successful partial crosses and the 12 parents were field evaluated using a 5 × 9 alpha lattice designs with two replications over two seasons in Tanzania. The tested genotypes exhibited significant (P

Forty-five African or Asian origin pearl millet populations bred either in Africa or Asia were investigated to generate information on heterotic pools. They were clustered into seven groups (G1 to G7) when genotyped, using 29 highly polymorphic SSRs. Fourteen parental populations representing these seven marker-based groups were crossed in diallel mating design to generate 91 population hybrids. The hybrids evaluated at three locations in India showed mean panmictic mid-parent heterosis (PMPH) and better-parent heterosis (PBPH) for grain yield ranging from − 21.7 to 62.08% and − 32.51 to 42.99%, respectively. Higher grain yield and heterosis were observed in G2 × G6 (2462 kg ha−1, 43.2%) and G2 × G5 (2455 kg ha−1, 42.8%) marker group crosses compared to the most popular Indian open-pollinated variety (OPV) ICTP 8203. Two heterotic groups, Pearl millet Population Heterotic Pool-1 (PMPHP-1) comprising G2 populations and Pearl millet Population Heterotic Pool-2 (PMPHP-2) comprising G5 and G6 populations, were identified based on hybrid performance, heterosis and combining ability among marker group crosses. Population hybrids from two heterotic groups, PMPHP-1 × PMPHP-2 demonstrated PMPH of 14.75% and PBPH of 6.8%. Populations of PMPHP-1 had linkages with either African or Asian origin populations, whereas PMPHP-2 composed of populations originating in Africa and later bred for Asian environments. Results indicated that parental populations from the two opposite heterotic groups can be used as base populations to derive superior inbred lines to develop high yielding hybrids/cultivars.

Whole‐genome resequencing (WGRS) of 396 lines, consisting of 104 hybrid parental lines and 292 germplasm lines, were used to study the molecular basis of mid‐parent heterosis (MPH) and to identify complementary heterotic patterns in pigeonpea [Cajanus cajan (L.) Millsp.] hybrids. The lines and hybrids were assessed for yield and yield‐related traits in multiple environments. Our analysis showed positive MPH values in 78.6% of hybrids, confirming the potential of hybrid breeding in pigeonpea. By using genome‐wide prediction and association mapping approaches, we identified 129 single nucleotide polymorphisms and 52 copy number variations with significant heterotic effects and also established a high‐yielding heterotic pattern in pigeonpea. In summary, our study highlights the role of WGRS data in the study and use of heterosis in crops where hybrid breeding is expected to boost selection gain in order to ensure global food security.

Exploring the natural genetic variability and its exploitation for improved Nitrogen Use Efficiency (NUE) in sorghum is one of the primary goals in the modern crop improvement programs. The integrated strategies include high-throughput phenotyping, next generation sequencing (NGS)-based genotyping technologies, and a priori selected candidate gene studies that help understand the detailed physiological and molecular mechanisms underpinning this complex trait. A set of sixty diverse sorghum genotypes was evaluated for different vegetative, reproductive, and yield traits related to NUE in the field (under three N regimes) for two seasons. Significant variations for different yield and related traits under 0 and 50% N confirmed the availability of native genetic variability in sorghum under low N regimes. Sorghum genotypes with distinct genetic background had interestingly similar NUE associated traits. The Genotyping-By-Sequencing based SNPs (>89 K) were used to study the population structure, and phylogenetic groupings identified three distinct groups. The information of grain N and stalk N content of the individuals covered on the phylogenetic groups indicated randomness in the distribution for adaptation under variable N regimes. This study identified promising sorghum genotypes with consistent performance under varying environments, with buffer capacity for yield under low N conditions. We also report better performing genotypes for varied production use—grain, stover, and dual-purpose sorghum having differential adaptation response to NUE traits. Expression profiling of NUE associated genes in shoot and root tissues of contrasting lines (PVK801 and HDW703) grown in varying N conditions revealed interesting outcomes. Root tissues of contrasting lines exhibited differential expression profiles for transporter genes [ammonium transporter (SbAMT), nitrate transporters (SbNRT)]; primary assimilatory (glutamine synthetase (SbGS), glutamate synthase (SbGOGAT[NADH], SbGOGAT[Fd]), assimilatory genes [nitrite reductase (SbNiR[NADH]3)]; and amino acid biosynthesis associated gene [glutamate dehydrogenase (SbGDH)]. Identification and expression profiling of contrasting sorghum genotypes in varying N dosages will provide new information to understand the response of NUE genes toward adaptation to the differential N regimes in sorghum. High NUE genotypes identified from this study could be potential candidates for in-depth molecular analysis and contribute toward the development of N efficient sorghum cultivars.

Sorghum (Sorghum bicolor L.) is a staple food crops in the arid and rainfed production ecologies. Sorghum plays a critical role in resilient farming and is projected as a smart crop to overcome the food and nutritional insecurity in the developing world. The development and characterisation of the sorghum pan-genome will provide insight into genome diversity and functionality, supporting sorghum improvement. We built a sorghum pan-genome using reference genomes as well as 354 genetically diverse sorghum accessions belonging to different races. We explored the structural and functional characteristics of the pan-genome and explain its utility in supporting genetic gain. The newly-developed pan-genome has a total of 35,719 genes, a core genome of 16,821 genes and an average of 32,795 genes in each cultivar. The variable genes are enriched with environment responsive genes and classify the sorghum accessions according to their race. We show that 53% of genes display presence-absence variation, and some of these variable genes are predicted to be functionally associated with drought adaptation traits. Using more than two million SNPs from the pan-genome, association analysis identified 398 SNPs significantly associated with important agronomic traits, of which, 92 were in genes. Drought gene expression analysis identified 1,788 genes that are functionally linked to different conditions, of which 79 were absent from the reference genome assembly. This study provides comprehensive genomic diversity resources in sorghum which can be used in genome assisted crop improvement.

Sorghum (Sorghum bicolorL.) is one of the most important food crops in the arid and rainfed production ecologies. It is a part of resilient farming and is projected as a smart crop to overcome the food and nutritional challenges in the developing world. The development and characterisation of the sorghum pan-genome will provide insight into genome diversity and functionality, supporting sorghum improvement. We built a sorghum pan-genome using reference genomes as well as 354 genetically diverse sorghum accessions belonging to different races. We explored the structural and functional characteristics of the pan-genome and explain its utility in supporting genetic gain. The newly-developed pan-genome has a total of 35,719 genes, a core genome of 16,821 genes and an average of 32,795 genes in each cultivar. The variable genes are enriched with environment responsive genes and classify the sorghum accessions according to their race. We show that 53% of genes display presence-absence variation, and some of these variable genes are predicted to be functionally associated with drought traits. Using more than two million SNPs from the pan-genome, association analysis identified 398 SNPs significantly associated with important agronomic traits, of which, 92 were in genes. Drought gene expression analysis identified 1,788 genes that are functionally linked to different conditions, of which 79 were absent from the reference genome assembly. This study provides comprehensive genomic diversity resources in sorghum which can be used in genome assisted crop improvement.

Nitrogen (N) is one of the primary macronutrients required for crop growth and yield. This nutrient is especially limiting in the dry and low fertility soils where pearl millet [Pennisetum glaucum (L.) R. Br] is typically grown. Globally, pearl millet is the sixth most important cereal grown by subsistence farmers in the arid and semi-arid regions of sub-Saharan Africa and the Indian subcontinent. Most of these agro-ecologies have low N in the root zone soil strata. Therefore, there is an immense need to identify lines that use nitrogen efficiently. A set of 380 diverse pearl millet lines consisting of a global diversity panel (345), parents of mapping populations (20), and standard checks (15) were evaluated in an alpha-lattice design with two replications, 25 blocks, a three-row plot for 11 nitrogen use efficiency (NUE) related traits across three growing seasons (Summer 2017, Rainy 2017, and Summer 2018) in an N-depleted precision field under three different N levels (0%-N0, 50%-N50, 100%-N100 of recommended N, i.e., 100 kg ha–1). Analysis of variance revealed significant genetic variation for NUE-related traits across treatments and seasons. Nitrogen in limited condition (N0) resulted in a 27.6 and 17.6% reduction in grain yield (GY) and dry stover yield (DSY) compared to N50. Higher reduction in GY and DSY traits by 24.6 and 23.6% were observed under N0 compared to N100. Among the assessed traits, GY exhibited significant positive correlations with nitrogen utilization efficiency (NUtE) and nitrogen harvest index (NHI). This indicated the pivotal role of N remobilization to the grain in enhancing yield levels. Top 25 N-insensitive (NIS-top grain yielders) and N-sensitive (NS-poor grain yielders) genotypes were identified under low N conditions. Out of 25 NIS lines, nine genotypes (IP 10820, IP 17720, ICMB 01222-P1, IP 10379, ICMB 89111-P2, IP 8069, ICMB 90111-P2, ICMV IS89305, and ICMV 221) were common with the top 25 lines for N100 level showing the genotype plasticity toward varying N levels. Low N tolerant genotypes identified from the current investigation may help in the identification of genomic regions responsible for NUE and its deployment in pearl millet breeding programs through marker-assisted selection (MAS).

Sorghum is widely grown as a failsafe crop in semi-arid regions particularly in post rainy season. Though the effect of drought on crop performance is studied widely there are few studies illustrating the association of fodder quality and agronomic traits under drought. To study the interactions we evaluated a set of 24 cultivars under drought for three years in post rainy season. The effect of drought was evident in delayed flowering (by 2 days) and reduce plant height (by 0.98 cm) compared to control. The fodder digestibility traits were reduced (in vitro organic matter digestibility by 2.25 times) under drought. All the plant growth and yield parameters recorded higher heritability compared to fodder quality parameters (

Millets are the strategic food crops in arid and drought-prone ecologies. Millets, by virtue of nature, are very well-adapted to drought conditions and able to produce sustainable yield. Millets have important nutrients that can help prevent micro-nutrient malnutrition. As a result of the adverse effect of climate change and widespread malnutrition, millets have attained a strategic position to sustain food and nutritional security. Although millets can adapt well to the drought ecologies where other cereals fail completely, the yield level is very low under stress. There is a tremendous opportunity to increase the genetic potential of millet crops in dry lands when the genetics of the drought-tolerance mechanism is fully explained. MicroRNAs (miRNAs) are the class of small RNAs that control trait expression. They are part of the gene regulation but little studied in millets. In the present study, novel miRNAs and gene targets were identified from the genomic resources of pearl millet, sorghum, foxtail millet, finger millet, and proso millet through in silico approaches. A total of 1,002 miRNAs from 280 families regulating 23,158 targets were identified using different filtration criteria in five millet species. The unique as well as conserved structural features and functional characteristics of miRNA across millets were explained. About 84 miRNAs were conserved across millets in different species combinations, which explained the evolutionary relationship of the millets. Further, 215 miRNAs controlling 155 unique major drought-responsive genes, transcription factors, and protein families revealed the genetics of drought tolerance that are accumulated in the millet genomes. The miRNAs regulating the drought stress through specific targets or multiple targets showed through a network analysis. The identified genes regulated by miRNA genes could be useful in developing functional markers and used for yield improvement under drought in millets as well as in other crops.

Brown planthopper (BPH), one of the most important pests of the rice (Oryza sativa) crop, becomes catastrophic under severe infestations and causes up to 60% yield loss. The highly disastrous BPH biotype in the Indian sub-continent is Biotype 4, which also known as the South Asian Biotype. Though many resistance genes were mapped until now, the utility of the resistance genes in the breeding programs is limited due to the breakdown of resistance and emergence of new biotypes. Hence, to identify the resistance genes for this economically important pest, we have used a multi-parent advanced generation intercross (MAGIC) panel consisting of 391 lines developed from eight indica founder parents. The panel was phenotyped at the controlled conditions for two consecutive years. A set of 27,041 cured polymorphic single nucleotide polymorphism (SNPs) and across-year phenotypic data were used for the identification of marker&ndash, trait associations. Genome-wide association analysis was performed to find out consistent associations by employing four single and two multi-locus models. Sixty-one SNPs were consistently detected by all six models. A set of 190 significant marker-associations identified by fixed and random model circulating probability unification (FarmCPU) were considered for searching resistance candidate genes. The highest number of annotated genes were found in chromosome 6 followed by 5 and 1. Ninety-two annotated genes identified across chromosomes of which 13 genes are associated BPH resistance including NB-ARC (nucleotide binding in APAF-1, R gene products, and CED-4) domain-containing protein, NHL repeat-containing protein, LRR containing protein, and WRKY70. The significant SNPs and resistant lines identified from our study could be used for an accelerated breeding program to develop new BPH resistant cultivars.

Pigeonpea is one of the important pulse crops grown in many states of India and plays a major role in sustainable food and nutritional security for the smallholder farmers. In order to overcome the productivity barrier the Translational Pigeonpea Genomics Consortium (TPGC) was established, representing research institutes from six different states (Andhra Pradesh, Karnataka, Madhya Pradesh, Maharashtra, Telangana, and Uttar Pradesh) of India. To enhance pigeonpea productivity and production the team has been engaged in deploying modern genomics approaches in breeding and popularizing modern varieties in farmers&rsquo, fields. For instance, new genetic stock has been developed for trait mapping and molecular breeding initiated for enhancing resistance to fusarium wilt and sterility mosaic disease in 11 mega varieties of pigeonpea. In parallel, genomic segments associated with cleistogamous flower, shriveled seed, pods per plant, seeds per pod, 100 seed weight, and seed protein content have been identified. Furthermore, 100 improved lines were evaluated for yield and desirable traits in multi-location trials in different states. Furthermore, a total of 303 farmers&rsquo, participatory varietal selection (FPVS) trials have been conducted in 129 villages from 15 districts of six states with 16 released varieties/hybrids. Additionally, one line (GRG 152 or Bheema) from multi-location trials has been identified by the All India Coordinated Research Project on Pigeonpea (AICRP-Pigeonpea) and released for cultivation by the Central Variety Release Committee (CVRC). In summary, the collaborative efforts of several research groups through TPGC is accelerating genetics gains in breeding plots and is expected to deliver them to pigeonpea farmers to enhance their income and improve livelihood.

With an aim of enhancing drought tolerance using a marker‐assisted backcrossing (MABC) approach, we introgressed the “QTL‐hotspot” region from ICC 4958 accession that harbors quantitative trait loci (QTLs) for several drought‐tolerance related traits into three elite Indian chickpea (Cicer arietinum L.) cultivars: Pusa 372, Pusa 362, and DCP 92‐3. Of eight simple sequence repeat (SSR) markers in the QTL‐hotspot region, two to three polymorphic markers were used for foreground selection with respective cross‐combinations. A total of 47, 53, and 46 SSRs were used for background selection in case of introgression lines (ILs) developed in genetic backgrounds of Pusa 372, Pusa 362, and DCP 92‐3, respectively. In total, 61 ILs (20 BC3F3 in Pusa 372; 20 BC2F3 in Pusa 362, and 21 BC3F3 in DCP 92‐3), with >90% recurrent parent genome recovery were developed. Six improved lines in different genetic backgrounds (e.g. BGM 10216 in Pusa 372; BG 3097 and BG 4005 in Pusa 362; IPC(L4‐14), IPC(L4‐16), and IPC(L19‐1) in DCP 92‐3) showed better performance than their respective recurrent parents. BGM 10216, with 16% yield gain over Pusa 372, has been released as Pusa Chickpea 10216 by the Central Sub‐Committees on Crop Standards, Notification and Release of Varieties of Agricultural Crops, Ministry of Agriculture and Farmers Welfare, Government of India, for commercial cultivation in India. In summary, this study reports introgression of the QTL‐hotspot for enhancing yield under rainfed conditions, development of several introgression lines, and release of Pusa Chickpea 10216 developed through molecular breeding in India.

Germplasm should be conserved in such a way that the genetic integrity of a given accession is maintained. In most genebanks, landraces constitute a major portion of collections, wherein the extent of genetic diversity within and among landraces of crops vary depending on the extent of outcrossing and selection intensity infused by farmers. In this study, we assessed the level of diversity within and among 108 diverse landraces and wild accessions using both phenotypic and genotypic characterization. This included 36 accessions in each of sorghum, pearl millet, and pigeonpea, conserved at ICRISAT genebank. We genotyped about 15 to 25 individuals within each accession, totaling 1,980 individuals using the DArTSeq approach. This resulted in 45,249, 19,052, and 8,211 high-quality single nucleotide polymorphisms (SNPs) in pearl millet, sorghum, and pigeonpea, respectively. Sorghum had the lowest average phenotypic (0.090) and genotypic (0.135) within accession distances, while pearl millet had the highest average phenotypic (0.227) and genotypic (0.245) distances. Pigeonpea had an average of 0.203 phenotypic and 0.168 genotypic within accession distances. Analysis of molecular variance also confirms the lowest variability within accessions of sorghum (26.3%) and the highest of 80.2% in pearl millet, while an intermediate in pigeonpea (57.0%). The effective sample size required to capture maximum variability and to retain rare alleles while regeneration ranged from 47 to 101 for sorghum, 155 to 203 for pearl millet, and 77 to 89 for pigeonpea accessions. This study will support genebank curators, in understanding the dynamics of population within and among accessions, in devising appropriate germplasm conservation strategies, and aid in their utilization for crop improvement.

Seed protein content (SPC) is an important grain quality trait, which impacts the nutritional importance of pigeonpea seed in the diet of over a billion people globally. The present study was carried out to determine variation in SPC and its relationships with some agronomic traits among 23 parental lines of different types of pigeonpea mapping populations. The parental lines were evaluated under field conditions during 2014-2015 growing season. A randomised complete block design in two replications was used. Data were recorded on SPC, days to first flower (DTF), plant height at maturity (PltH), number of pods per plant (NPP), number of seeds per pod (NSP), hundred-seed weight (SW) and seed yield per plant (SY). There were significant differences among genotypes for all traits. Broad-sense heritability was 0.693 for SPC but ranged from 0.519 (NPP) to 0.999 (DTF) while genetic advance was 2.4% for SPC but ranged from 1.2 % (NSP) to 141.2 % (SY), and genetic gain ranged from 11.0 % (SPC) to 230.0 % (SY). Simple correlation showed that SPC is only significantly but negatively correlated with SW (r = -0.30, P < 0.05), while path analyses revealed that SPC is negatively associated SW and NPP but positively with DTF, PltH, NSP and SY. It is concluded that genetic variation for SPC and agronomic traits exist among pigeonpea genotypes studied. The variation is accompanied by both favourable and unfavourable relationships of SPC with the agronomic traits.

Three bacteria, IC-59, IC-76A and IC-2002, isolated from the nodules of chickpea, were characterized for nodulation, nitrogen fixation, plant growth-promoting (PGP) and yield traits in five cultivars of chickpea such as BG256, RSG888, Subhra, K850 and ICCV2. All the bacteria produced cellulase, protease, β-1,3-glucanase, indole acetic acid, siderophore, hydro cyanic acid and 1-aminocyclopropane-1-carboxylate deaminase while none produced lipase and chitinase. The 16 S rDNA gene sequences of IC-59, IC-76A and IC-2002 were found to match closely with Rhizobium pusense, Paraburkholderia kururiensis and Stenotrophomonas maltophilia, respectively. The three bacteria nodulated all the cultivars of chickpea well, amplified nifH gene and fixed nitrogen. Under greenhouse conditions at 30 and 45 days after sowing, treatment of five cultivars of chickpea with bacterial cultures IC-59, IC-76A and IC-2002, enhanced the nodule number (up to 45%, 38% and 43%), nodule weight (up to 31%, 15% and 39%), shoot weight (11%, 16% and 14%) and root weight (37%, 48% and 62%), respectively, over the un-inoculated control. At crop maturity, IC-59, IC-76A and IC-2002 were found to enhance the shoot weight (16%, 40% and 26%), pod number (37%, 69% and 81%), pod weight (17%, 45% and 49%), seed number (21%, 31% and 39%) and seed weight (14%, 56% and 65%), respectively, over the un-inoculated control. Among the five cultivars, Subhra was found to enhance most of the PGP traits when treated with the three diazotrophic bacteria. It is concluded that the three diazotrophic bacteria could be potentially exploited for improving nodulation, nitrogen fixation, PGP and yields of chickpea.

Pearl millet is a non-model grain and fodder crop adapted to extremely hot and dry environments globally. In India, a great deal of public and private sectors’ investment has focused on developing pearl millet single cross hybrids based on the cytoplasmic-genetic male sterility (CMS) system, while in Africa most pearl millet production relies on open pollinated varieties. Pearl millet lines were phenotyped for both the inbred parents and hybrids stage. Many breeding efforts focus on phenotypic selection of inbred parents to generate improved parental lines and hybrids. This study evaluated two genotyping techniques and four genomic selection schemes in pearl millet. Despite the fact that 6× more sequencing data were generated per sample for RAD-seq than for tGBS, tGBS yielded more than 2× as many informative SNPs (defined as those having MAF > 0.05) than RAD-seq. A genomic prediction scheme utilizing only data from hybrids generated prediction accuracies (median) ranging from 0.73-0.74 (1000-grain weight), 0.87-0.89 (days to flowering time), 0.48-0.51 (grain yield) and 0.72-0.73 (plant height). For traits with little to no heterosis, hybrid only and hybrid/inbred prediction schemes performed almost equivalently. For traits with significant mid-parent heterosis, the direct inclusion of phenotypic data from inbred lines significantly (P < 0.05) reduced prediction accuracy when all lines were analyzed together. However, when inbreds and hybrid trait values were both scored relative to the mean trait values for the respective populations, the inclusion of inbred phenotypic datasets moderately improved genomic predictions of the hybrid genomic estimated breeding values. Here we show that modern approaches to genotyping by sequencing can enable genomic selection in pearl millet. While historical pearl millet breeding records include a wealth of phenotypic data from inbred lines, we demonstrate that the naive incorporation of this data into a hybrid breeding program can reduce prediction accuracy, while controlling for the effects of heterosis per se allowed inbred genotype and trait data to improve the accuracy of genomic estimated breeding values for pearl millet hybrids.

Genetic distances between hybrid parents based on phenotypic traits and molecular markers were investigated to assess their relationship with heterosis for grain and stover yield and other traits in pearl millet (Pennisetum glaucum [L.] R. Br.). Fifty-one hybrids developed using 101 hybrid parents (B and R lines) and showing a wide range of genetic distance between their parents based on eight phenotypic traits and 28–38 SSRs were evaluated in two sets for two seasons. The correlation between Euclidean distance (phenotypic distance, ED) and simple matching distance (molecular distance, SM) for parents of both sets was low but positive and significant (r = 0.2, P

Post flowering stalk rot (PFSR) is one of the major biotic constraints to maize production in tropical and sub-tropical environments. It is a complex disease caused by multiple pathogens, among which Fusarium moniliforme and Macrophomina phaseolina are the major ones that cause severe yield losses in the Asian tropics. A set of maize inbred lines was evaluated at two locations for Fusarium stalk rot (FSR) and Macrophomina stalk rot (MSR). Based on line evaluation trials, resistant and susceptible lines were selected and crossed following a Diallel mating design IV to study the gene action for resistance to these stalk rots and the estimating the combining ability of inbred lines. A 9 × 9 diallel (Diallel-A) produced 36 hybrids for studying FSR resistance, and a 12 × 12 diallel (Diallel-B) produced 66 hybrids to analyse the resistance towards both FSR and MSR. These hybrids were evaluated at two locations for MSR and one location for FSR with artificial inoculation. The hybrids differed significantly for FSR (p

The All India Coordinated Rice Improvement Project of ICAR-Indian Institute of Rice Research, Hyderabad organizes multi-location testing of elite lines and hybrids to test and identify new rice cultivars for the release of commercial cultivation in India. Data obtained from Initial Hybrid Rice Trials of three years were utilized to understand the genotype × environment interaction (GEI) patterns among the test locations of five different agro-ecological regions of India using GGE and AMMI biplot analysis. The combined analysis of variance and AMMI ANOVA for a yield of rice hybrids were highly significant for GEI. The GGE biplots first two PC explained 54.71%, 51.54% and 59.95% of total G + GEI variation during 2010, 2011 and 2012, respectively, whereas AMMI biplot PC1 and PC2 explained 46.62% in 2010, 36.07% in 2011 and 38.33% in 2012 of the total GEI variation. Crossover interactions, i.e. genotype rank changes across locations were observed. GGE biplot identified hybrids, viz. PAN1919, TNRH193, DRH005, VRH639, 26P29, Signet5051, KPH385, VRH667, NIPH101, SPH497, RH664 Plus and TNRH222 as stable rice hybrids. The discriminative locations identified in different test years were Coimbatore, Maruteru, VNR, Jammu, Raipur, Ludhiana, Karjat and Dabhoi. The AMMI1 biplot identified the adaptable rice hybrids viz., CNRH102, DRH005, NK6303, NK6320, DRRH78, NIPH101, Signet5050, BPH115, Bio452, NPSH2003, and DRRH83. The present study demonstrated that AMMI and GGE biplots analyses were successful in assessing genotype by environment interaction in hybrid rice trials and aided in the identification of stable and adaptable rice hybrids with higher mean and stable yields.

The dearth of proper delineation for energy sorghum cultivation has led to a prerequisite for evaluation and identification of test environments for the newly developed lines. This becomes of vital importance as the biomass yield is highly influenced by genotype and environmental (G × E) interactions. Several agronomic traits were considered to assess the biomass yield and the combined analysis of variance for G (genotype), L (location) and interaction effect of G × L. The variations in the yield caused by the interaction of G × L are very essential to acquire knowledge on the specific adaptation of a genotype. Thus, the multi-location trials conducted across locations and years have helped to identify the stable environments with specific adaptation for biomass sorghum. The presence of close association between the test locations suggested that the same information about the genotypes could be obtained from fewer test environments, and hence the potential to reduce evaluation costs. The two genotypes—IS 13762 and ICSV 25333—have shown stable performance for biomass traits across all the locations, in comparison with CSH 22SS (check). The top ten entries with stable and better performance for fresh biomass yield, dry biomass yield, grain yield and theoretical ethanol yield were ICSV 25333, IS 13762, CSH 22SS, IS 25302, IS 25301, IS 27246, IS 16529, DHBM2, ICSSH 28 and IS 17349.

A survey was conducted in 2014 to determine the prevalence of fungal diseases on sorghum across different agroecological zones in Tanzania and Uganda. In Tanzania, 37 sorghum fields were sampled in Dodoma and Singida Provinces, representing the central drier areas, and in Simiyu, Shinyanga, Mwanza, and Mara Provinces, representing the lake-zone region. In Uganda, 134 fields were sampled across four agroecological zones of Teso, Western, Northern, and West Nile. Farmers were purposively selected, and at least 30 plants per field along two diagonal transects were visually assessed for disease. Ten and 14 diseases were identified in Tanzania and Uganda, respectively. Among the major diseases identified, those more prevalent in Tanzania than in Uganda were leaf blight caused by Setosphaeria turcica (P = 0.0031) and rust caused by Puccinia purpurea (P < 0.0001). Major diseases more prevalent in Uganda than in Tanzania were anthracnose caused by Colletotrichum sublineola (P = 0.0207) and zonate leaf spot caused by Gloeocercospora sorghi (P = 0.0312). We report for the first time the occurrence of ladder leaf spot caused by Cercospora fusimaculans in Uganda and confirm its occurrence in Tanzania. This is the first comprehensive sorghum disease survey report in over 15 years in both countries.

The staple crops, maize, sorghum, bambara nut, groundnut, and sunflower common in semi-arid agro-pastoral farming systems of central Tanzania are prone to aflatoxin contamination. Consumption of such crop produce, contaminated with high levels of aflatoxin B1 (AFB1), affects growth and health. In this paper, aflatoxin contamination in freshly harvested and stored crop produce from central Tanzania was examined, including the efficacy of aflatoxin mitigation technologies on grain/kernal quality. A total of 312 farmers were recruited, trained on aflatoxin mitigation technologies, and allowed to deploy the technologies for 2 years. After 2 years, 188 of the 312 farmers were tracked to determine whether they had adopted and complied with the mitigation practices. Aflatoxigenic Aspergillus flavus and aflatoxin B1 contamination in freshly harvested and stored grains/kernels were assessed. A. flavus frequency and aflatoxin production by fungi were assayed by examining culture characteristics and thin-layer chromatography respectively. AFB1 was assayed by enzyme-linked immunosorbent assay. The average aflatoxin contamination in freshly harvested samples was 18.8 μg/kg, which is above the acceptable standard of 10 μg/kg. Contamination increased during storage to an average of 57.2 μg/kg, indicating a high exposure risk. Grains and oilseeds from maize, sorghum, and sunflower produced in aboveground reproductive structures had relatively low aflatoxin contamination compared to those produced in geocarpic structures of groundnut and bambara nut. Farmers who adopted recommended post-harvest management practices had considerably lower aflatoxin contamination in their stored kernels/grains. Furthermore, the effects of these factors were quantified by multivariate statistical analyses. Training and behavioral changes by farmers in their post-harvest practice minimize aflatoxin contamination and improve food safety. Moreover, if non-trained farmers receive mitigation training, aflatoxin concentration is predicted to decrease by 28.9 μg/kg on average.

Genetic diversity in the breeding materials is an essential component to improve the efficiency of any crop improvement programme. In present study, 150 seed and restorer parents were evaluated for grain yield and its component traits at two diverse agro-ecologies CCSHAU-Hisar and ICRISAT-Patancheru. Analysis of variance revealed significant differences among hybrid parents for all traits. Clustering of hybrid parents clearly partitioned almost all the B- and R-lines into separate groups indicating B- and R-lines to be genetically distant from each other. Further, seed (B-lines) and restorer (R-lines) parents were found distributed in four clusters each, and hybrid parents having same plant type (having similar set of specific traits) were found in same cluster. Significant numbers of hybrid parents having common parent in their pedigrees were found in same cluster. Cluster B-IV of B-lines and cluster R-III of R-lines had higher grain yield and above average performance for other grain linked traits. Grain yield was found to have highly positive significant correlation with all the traits under study for both B- and R-lines, except for effective tillers plant-1. Stover yield followed by panicle girth and panicle length had highest positive direct effect on grain yield.

Mungbean (Vigna radiata (L.) Wilczek) is an important pulse crop in India. A major constraint for improved productivity is the yield loss caused by mungbean yellow mosaic disease (MYMD). This disease is caused by several begomoviruses which are transmitted by the whitefly Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae). The objective of this study was to identify the predominant begomoviruses infecting mungbean and the major cryptic species of B. tabaci associated with this crop in India. The indigenous B. tabaci cryptic species Asia II 1 was found dominant in Northern India, whereas Asia II 8 was found predominant in Southern India. Repeated samplings over consecutive years indicate a stable situation with, Mungbean yellow mosaic virus strains genetically most similar to a strain from urdbean (MYMV-Urdbean) predominant in North India, strains most similar to MYMV-Vigna predominant in South India, and Mungbean yellow mosaic India virus (MYMIV) strains predominant in Eastern India. In field studies, mungbean line NM 94 showed a high level of tolerance to the disease in the Eastern state of Odisha where MYMIV was predominant and in the Southern state of Andhra Pradesh where MYMV-Vigna was predominant, but only a moderate level of tolerance in the Southern state of Tamil Nadu. However, in Northern parts of India where there was high inoculum pressure of MYMV-Urdbean during the Kharif season, NM 94 developed severe yellow mosaic symptoms. The identification of high level of tolerance in mungbean lines such as ML 1628 and of resistance in black gram and rice bean provides hope for tackling the disease through resistance breeding.

Micronutrient malnutrition is one of the major health problem, especially iron (Fe) and zinc (Zn) deficiencies that are widespread coupled with inadequate food supply in the developing world. Pearl millet grains are a good source of Fe and Zn elements making it a potential staple crop for overcoming hidden-hunger and micronutrient deficiencies. Breeding pearl millet with high levels of grain Zn and Fe contents represents a major opportunity to enhance the intake of these minerals for poor and malnourished people. A precise understanding of the genetic variability, correlation of mineral nutrients, genotype × environment (G × E) interaction is important for developing improved lines with high Fe and Zn content. To get fair estimates, we used a bi-parental recombinant inbred lines (RIL) mapping population representing F2 phenotypic variance. A total of 317 RILs were evaluated for grain iron and zinc content in two seasons, Summer 2016 (E1) and Summer 2017 (E2). The result from the analysis of variance exhibited a large variability for grain Fe and Zn content across the two environments. The G × E for high grain Fe were significant at P 0.01. The mean performance across the two environments data for grain Fe ranged from 22.9 to 154.5 mg kg-1 (ppm) and Zn content ranged from 19.3 to 121 mg kg-1. The correlation coefficient for grain Fe and Zn was 0.9, and 0.8 and across the two (E1 and E2) environments. The value of correlation coefficient (0.9) was found to be highly significant at P 0.01 level, that indicated good opportunities for simultaneous genetic improvement of both iron and zinc contents in pearl millet.

Fusarium wilt (Fusarium oxysporum f. sp. ciceris) of chickpea is the major limitation to chickpea production worldwide. As the nature of the pathogen is soil borne, exploitation of host plant resistance is the most suitable and economical way to manage this disease. Present study was therefore conducted with an aim to find new, stable and durable sources of resistance of chickpea against Fusarium wilt through multi-environment and multi-year screening. During 2007/2008 crop season, 130 promising genotypes having

Dry root rot (DRR), caused by Macrophomina phaseolina, is a prevalent disease of mungbean in Myanmar, and an emerging problem in South Asia. The pathogen is a polyphagous necrotroph, survives in the soil for many years that results disease mitigation difficult. Managing DRR in mungbean through an integrated approach has been suggested, and the use of resistant varieties is one of the economical methods. The present study aimed to identify sources of resistance against DRR from a mungbean mini-core collection and to characterize the associated M. phaseolina isolates from India and Myanmar. Evaluation of the 296 mungbean mini-core accessions against the isolate MP1 by paper towel method identified 29 accessions with DRR resistance (disease scores: ≤ 3), and 18 of them with the consistent resistance in the repeated experiment. During the screening of 18 resistant accessions in the glasshouse, nine accessions were found DRR resistance in repeated sick pot experiments with ≤10% disease incidence. A subset of 30 accessions was selected from the mini-core collection based on their in vitro DRR reactions. These accessions were evaluated for DRR resistance in the field in Yezin, Myanmar in 2018 and 2019. Out of the 30 accessions, ten accessions were found DRR resistance with ≤10% disease incidence in both years of evaluations. Pooled analysis of percent disease incidence data of 15 accessions common in both glasshouse and field revealed the stability of accessions VI001509AG, VI001244AG, and VI001400AG for DRR resistance across years and locations. The three resistant accessions along with a susceptible check VC693088 were re-evaluated by paper towel method against nine additional M. phaseolina isolates from India (MP3-MP11). The accessions VI001509AG and VI001400AG were resistant to all nine isolates, while accession VI001244AG was resistant to MP5, MP6, and MP7 isolates. These accessions could be used in mungbean DRR resistance breeding programs.

Dry root rot (DRR) is an important emerging disease of mungbean caused by fungus Macrophomina phaseolina. The disease is seed and soil-borne and hence management is difficult. Exploitation of host resistance could be a good option to manage the disease. The objectives of this study were to characterize the isolates of M. phaseolina from three legume crops and to identify resistant sources against DRR of mungbean. Isolates of M. phaseolina from mungbean, urdbean, and vegetable soybean were identified using morphological characteristics and sequencing internal transcribed sequence (ITS) region of 18S rRNA. Isolates of M. phaseolina from urdbean and vegetable soybean were inoculated on susceptible check genotype of mungbean to assess their pathogenicity. Forty three mungbean genotypes were screened against M. phaseolina isolate of mungbean using the paper towel method to identify sources of resistance. Among these genotypes, 9 were resistant in repeated experiment, with disease score ranging from 1.9 to 3.0. Resistant genotypes showing lower disease score, namely IPM99-125, EC693368, and EC693369, were further screened using the sick pot method to confirm their resistance. Among these three genotypes, IPM99-125 showed consistently higher plant survival rate followed by EC693368 and EC693369 as compared to susceptible checks (VC3960-88, KPS1). In addition, these three genotypes were resistant when screened with two strains of M. phaseolina isolated from urdbean and vegetable soybean, with IPM99-125 having lower disease score. The mungbean genotype IPM99-125 could be useful in mungbean breeding programs to develop root rot-resistant varieties.

Pea, one of the founder crops from the Near East, has two wild species: Pisum sativum subsp. elatius, with a wide distribution centered in the Mediterranean, and P. fulvum, which is restricted to Syria, Lebanon, Israel, Palestine and Jordan. Using genome wide analysis of 11,343 polymorphic single nucleotide polymorphisms (SNPs) on a set of wild P. elatius (134) and P. fulvum (20) and 74 domesticated accessions (64 P. sativum landraces and 10 P. abyssinicum), we demonstrated that domesticated P. sativum and the Ethiopian pea (P. abyssinicum) were derived from different P. elatius genepools. Therefore, pea has at least two domestication events. The analysis does not support a hybrid origin of P. abyssinicum, which was likely introduced into Ethiopia and Yemen followed by eco-geographic adaptation. Both P. sativum and P. abyssinicum share traits that are typical of domestication, such as non-dormant seeds. Non-dormant seeds were also found in several wild P. elatius accessions which could be the result of crop to wild introgression or natural variation that may have been present during pea domestication. A sub-group of P. elatius overlaps with P. sativum landraces. This may be a consequence of bidirectional gene-flow or may suggest that this group of P. elatius is the closest extant wild relative of P. sativum.

Pearl millet is a climate resilient crop and one of the most widely grown millets worldwide. Heterotic hybrid development is one of the principal breeding objectives in pearl millet. In a maiden attempt to identify heterotic groups for grain yield, a total of 343 hybrid parental [maintainer (B-) and restorer (R-)] lines were genotyped with 88 polymorphic SSR markers. The SSRs generated a total of 532 alleles with a mean value of 6.05 alleles per locus, mean gene diversity of 0.55, and an average PIC of 0.50. Out of 532 alleles, 443 (83.27%) alleles were contributed by B-lines with a mean of 5.03 alleles per locus. R-lines contributed 476 alleles (89.47%) with a mean of 5.41, while 441 (82.89%) alleles were shared commonly between B- and R-lines. The gene diversity was higher among R-lines (0.55) compared to B-lines (0.49). The unweighted neighbor-joining tree based on simple matching dissimilarity matrix obtained from SSR data clearly differentiated B- lines into 10 sub-clusters (B1 through B10), and R- lines into 11 sub-clusters (R1 through R11). A total of 99 hybrids (generated by crossing representative 9 B- and 11 R- lines) along with checks were evaluated in the hybrid trial. The 20 parents were evaluated in the line trial. Both the trials were evaluated in three environments. Based on per se performance, high sca effects and standard heterosis, F1s generated from crosses between representatives of groups B10R5, B3R5, B3R6, B4UD, B5R11, B2R4, and B9R9 had high specific combining ability for grain yield compared to rest of the crosses. These groups may represent putative heterotic gene pools in pearl millet.

Chitin is the second most plenteous polysaccharide in nature after cellulose, present in cell walls of several fungi, exoskeletons of insects, and crustacean shells. Chitin does not accumulate in the environment due to presence of bacterial chitinases, despite its abundance. These enzymes are able to degrade chitin present in the cell walls of fungi as well as the exoskeletons of insect. They have shown being the potential agents for biological control of the plant diseases caused by various pathogenic fungi and insect pests and thus can be used as an alternative to chemical pesticides. There has been steady increase in demand of chitin derivatives, obtained by action of chitinases on chitin polymer for various industrial, clinical, and pharmaceutical purposes. Hence, this review focuses on properties and applications of chitinases starting from bacteria, followed by fungi, insects, plants, and vertebrates. Designing of chitinase by applying directed laboratory evolution and rational approaches for improved catalytic activity for cost-effective field applications has also been explored.

Sorghum (Sorghum bicolor L. Moench) is a major food crop grown in dry lands and sub-humid areas of East Africa. A study was conducted between 2010 to 2012 in dry lands (Miwaleni, Kiboko) and sub-humid (Ukiriguru) environments to identify parents for hybrid production. It involved 121 lines from ICRISAT and 121 hybrids developed from 36 male sterile lines and 42 restorer lines in a line × tester crossing. Experiments were planted in an alpha lattice design with three replications. Analysis revealed significant (P < 0.05) differences between parents and between crosses for yield and yield components, indicative of potentiality for exploitation. Line IESV23010 expressed best (-6.5) general combing ability (GCA) for days to 50% flowering (DAF). Highest general combiner for height was -55.4 expressed in ICSR24007 and for yield was 382.8 expressed in IESV92156DL. The crosses SDSA4×ICSR43 and SDSA4×ICSR59059 exhibited high and significant specific combining ability (SCA) for DAF. Lines IESB2 and ICSB44 were suited to sub-humid, whereas BTX623, ICSB15 and ICSB6 to dry lands environments. Testers IESV91104DL, IESV91131DL, ICSR93034 were well suited to dry lands whereas KARI-MTAMA1 and IESV23019 to sub-humid environments. The parents identified could be used to produce hybrids and varieties for the dry lands and sub-humid environments. Key words: Combining ability, lines, restorers, sorghum, top-cross hybrids.

In cytoplasmic genetic male sterility-based (CGMS) hybrid seed production, instability of expression of male-sterility and fertility restoration across a wide range of environments are two of the major difficulties. Therefore, the present study was carried out to investigate the stability of male sterility of nine CGMS lines under three dates of sowing and the fertility restoration of 10 CGMS-based pigeonpea (Cajanus cajan (L.) Millsp.) hybrids at three different locations. Significant variability existed for pollen fertility among hybrids and sterility among cytoplasmic male sterile (CMS) lines. All the hybrids except ICPH 3494 and ICPH 3491 exhibited high (>80%) pollen fertility across locations. Hybrids ICPH 2671, ICPH 2740, and ICPH 3933 had 100% male-fertile plants across locations. All the CMS lines had completely male-sterile plants across sowing dates. The CMS lines BRG1 A, Hy3C A, BRG3 A, and TTB7 A exhibited 100% pollen sterility at different sowing dates. The pooled analysis revealed a signific...

ICRISAT’s pearl millet (Pennisetum glaucum (L.) R. Br.) breeding program at Patancheru, India, has developed genetically diverse hybrid parents since 1980s. The present study investigated genetic diversity pattern between two groups of parents in this program, bred till 2004 and developed during 2004-2010. Combined analysis of 379 hybrid parents (current 166 parents and 213 previously developed hybrid parents) carried out using a set of highly polymorphic 28 SSRs detected 12.7 alleles per locus. An average of 8.5 and 8.7 SSR alleles per locus were found in previously developed and current parents, respectively, indicating marginal improvement in the levels of genetic diversity of hybrid parents in this program. Distance matrix differentiated these current and previously developed hybrid parents into 2 separate clusters, indicating infusion of new genetic variability over time as reflected by development of more genotype-specific alleles. Also, the seed and restorer parents were found clearly separated from each other in both the sets with few crossovers, indicating existence of two diverse and broad-based pools in hybrid parents of pearl millet. Restorer parents (R-lines) were found more diverse than seed parents (B-lines), as higher average gene diversity was detected among R-lines (0.70) than B-lines (0.56), though variation between B- and R-lines was found reduced in newly developed lines to 9.22% from 16.98% in previously developed lines. Results suggested that newly developed lines were as much divergent when compared with previously developed lines, indicating that current ICRISAT pearl millet breeding program was moving towards development of diverse new hybrid parental lines. The study suggested use of trait-specific donors in B- and R-lines separately to maintain sufficient genetic distance between seed and restorer breeding lines. It was pointed out to cross parents having higher genetic distance within the seed (B-lines) and restorer (R-lines) breeding programs to derive diverse and productive hybrid parental lines in future.

The low grain iron and zinc densities are well documented problems in food crops, affecting crop nutritional quality especially in cereals. Sorghum is a major source of energy and micronutrients for majority of population in Africa and central India. Understanding genetic variation, genotype × environment interaction and association between these traits is critical for development of improved cultivars with high iron and zinc. A total of 336 sorghum RILs (Recombinant Inbred Lines) were evaluated for grain iron and zinc concentration along with other agronomic traits for 2 years at three locations. The results showed that large variability exists in RIL population for both micronutrients (Iron = 10.8 to 76.4 mg kg−1 and Zinc = 10.2 to 58.7 mg kg−1, across environments) and agronomic traits. Genotype × environment interaction for both micronutrients (iron and zinc) was highly significant. GGE biplots comparison for grain iron and zinc showed greater variation across environments. The results also showed that G × E was substantial for grain iron and zinc, hence wider testing needed for taking care of G × E interaction to breed micronutrient rich sorghum lines. Iron and zinc concentration showed high significant positive correlation (across environment = 0.79; p < 0.01) indicating possibility of simultaneous effective selection for both the traits. The RIL population showed good variability and high heritabilities (>0.60, in individual environments) for Fe and Zn and other traits studied indicating its suitability to map QTL for iron and zinc.

Botrytis grey mould (BGM), caused by Botrytis cinerea Pers. Ex. Fr., is a destructive foliar disease of chickpea (Cicer arietinum L.) worldwide. Disease management through host-plant resistance is the most effective and economic option to manage this disease. The objective of this study was to identify new sources of resistance to BGM, validate their stability across environments and determine the magnitude of G × E interaction. One hundred and nine chickpea genotypes with moderate levels of resistance (BGM severity ≤5.0 on a 1–9 scale) were selected from the preliminary evaluation of 412 genotypes including germplasm and breeding lines under controlled environmental conditions in 2004–2005 at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India. In order to validate resistance stability, an ‘International Botrytis Grey Mould Nursery’ (IBGMN) was constituted with 25 genotypes and tested in multi-environments for BGM resistance at two locations (Gurdaspur and Pantnagar) in India for 4 years and two locations (Tarahara and Rampur) in Nepal for 3 years. Additive main effects and multiplicative interaction (AMMI) analysis showed significant genotype (G), environment (E) and G × E interaction (p < 0.0001) with largest contribution by environment (47.36%). The first two principal component axes were significant, and contributed 48.21% to the total G × E interaction. The AMMI biplot analysis allowed the selection of five genotypes ICCV 96859, ICCV 96853, ICCV 05604, ICCV 96852 and ICCV 05605 with low BGM severity (between 3.7 and 4.7 on 1–9 scale) and moderate stability. Genotype ICCV 96859 having least disease severity and moderate stability could be highlighted and exploited in chickpea resistance breeding programmes

Pearl millet [Pennisetum glaucum (L.) R. Br.] is grown under a wide range of environmental conditions in India. The All India Coordinated Pearl Millet Improvement Project (AICPMIP) has the responsibility of testing and releasing pearl millet cultivars adapted to such conditions. As a part of this process, AICPMIP has divided the entire pearl millet growing regions into three different zones (A1, A, and B) based on the rainfall pattern and local adaptation of the crop. This study was conducted to define the presently used test locations into possible mega-environments and to identify essential test locations for cost-effective evaluation of pearl millet cultivars. Grain yield data of different sets of 34 to 45 medium-maturity pearl millet hybrids tested at 29 to 34 locations during 2006 to 2008 were analyzed using genotype main effects and genotype × environment interaction biplot method. Two distinct pearl millet mega-environments with consistent grouping of locations across the years and corresponding to AICPMIP’s designated A and B zones were identified. No such consistent grouping of locations corresponding to AICPMIP’s designated A1 zone was, however, observed. Based on the discriminating ability, uniqueness, and research resources, 13 locations were identified as essential test locations for evaluation across the two mega-environments. Testing at these locations appeared to provide good coverage of the whole pearl millet growing areas of India. Based on these findings, it is suggested to conduct initial yield trials at identified 13 locations across all the pearl millet growing zones represented by two mega-environments followed by testing of selected hybrids with specific adaptation in their respective adaptation zones.

The first sorghum [Sorghum bicolor (L.) Moench] hybrids based on West African Guinea-race-derived parents were created to enhance farmer’s food security and income through increased yields. To assess their performance, eight hybrids, six experimental pure-line cultivars, one pure-line check (Lata), and a highly adapted landrace cultivar (Tieble) were evaluated in 27 farmer-managed and two on-station yield trials in Mali, West Africa, from 2009 to 2011. The hybrids were confirmed to have photoperiod sensitivity similar to the well-adapted Guinea landrace check cultivar. Genotypic differences for on-farm grain yield were highly significant and genotype × environment crossover interactions were limited. The yield superiorities of individual hybrids, relative to the landrace check, ranged from 17 to 37% over the 27 on-farm trials. The three top yielding hybrids showed 30% yield advantages across productivity levels, with absolute yield advantages averaging 380 kg ha−1 under lower (1.0–1.5 t ha−1) and 660 kg ha−1 under higher (2.0–3.5 t ha−1) productivity conditions. A mean male-parent (better parent) heterosis of 26% was observed for the four hybrids having Lata as a male parent. As the hybrids studied here were obtained with a low intensity of selection using a limited number of parents, even greater yield superiorities may be attained with development of distinct parental pools and scaled-up hybrid breeding.

Increased global interest in biofuel feedstocks made sweet sorghum as one of the prominent energy crop suitable for both first and second generation biofuel production. An attempt has been made to critically identify the factors contributing to biomass yield and their interrelationship in sweet sorghum plant (main) and ratoon trials. The genotypes ICSSH 28, ICSSH 58, ICSA 749 × SPV 1411, B-24 and ICSV 93046 exhibited higher ratooning efficiency. It was observed that higher the ratooning efficiency lower will be the difference between the growing degree days (GDD) of main and ratoon crop. GDD can be used as one of the selection criteria in breeding programs aiming for enhanced biomass and ratooning efficiency.

Fusarium wilt (FW) and Ascochyta blight (AB) are two important diseases of chickpea which cause 100 % yield losses under favorable conditions. With an objective to validate and/or to identify novel quantitative trait loci (QTLs) for resistance to race 1 of FW caused by Fusarium oxysporum f. sp. ciceris and AB caused by Ascochyta rabiei in chickpea, two new mapping populations (F2:3) namely ‘C 214’ (FW susceptible) × ‘WR 315’ (FW resistant) and ‘C 214’ (AB susceptible) × ‘ILC 3279’ (AB resistant) were developed. After screening 371 SSR markers on parental lines and genotyping the mapping populations with polymorphic markers, two new genetic maps comprising 57 (C 214 × WR 315) and 58 (C 214 × ILC 3279) loci were developed. Analysis of genotyping data together with phenotyping data collected on mapping population for resistance to FW in field conditions identified two novel QTLs which explained 10.4–18.8 % of phenotypic variation. Similarly, analysis of phenotyping data for resistance to seedling resistance and adult plant resistance for AB under controlled and field conditions together with genotyping data identified a total of 6 QTLs explaining up to 31.9 % of phenotypic variation. One major QTL, explaining 31.9 % phenotypic variation for AB resistance was identified in both field and controlled conditions and was also reported from different resistant lines in many earlier studies. This major QTL for AB resistance and two novel QTLs identified for FW resistance are the most promising QTLs for molecular breeding separately or pyramiding for resistance to FW and AB for chickpea improvement.

Ascochyta blight (AB) caused by Ascochyta rabei (Pass.) Labr. is one of the most important constraints that limits the productivity of chickpea (Cicer arietinum L.). The absence of high levels of stable resistant sources to the pathogen has necessitated the continued search and identification of new sources of resistance. The main aim of this work was to identify new sources of resistance to AB and validate their stability across multi-environments. A collection of 424 elite chickpea genotypes were evaluated for AB resistance under controlled environmental conditions in 2005–2006 at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India. Fifty-one genotypes with AB severity ≤3.0 (based on the 1–9 scale) were selected for a second round of evaluation in 2006–2007 at ICRISAT. Based on the results obtained during both years, an Ascochyta Blight Nursery (ABN) was established to evaluate the selected 29 chickpea genotypes, including 4 germplasm lines, 24 breeding lines and a highly susceptible line. The nursery was evaluated at 3 locations (Almora, Dhaulakuan and Ludhiana) in India over three crop seasons (2007–2008, 2008–2009 and 2009–2010) and under controlled environment conditions at ICRISAT to further confirm the stable performance of these genotypes. Analysis of variance revealed highly significant effects of year, location (year), genotype and genotype × location (year) interaction. The genotype and genotype × environment (GGE) biplot analyses of multi-environment data showed that resistance of five genotypes (EC 516934, ICCV 04537, ICCV 98818, EC 516850 and EC 516971) had mean disease severity ≤3.0 on the 1–9 scale and the reactions were consistent across the environments. Genotype EC 516934 was found resistant to AB at the seedling stage in the controlled environment at ICRISAT. The remaining genotypes showed moderately resistant reaction (3.0–5.0) to AB under controlled environment conditions. A significant positive correlation was found between the performance of the genotypes under controlled environment and field screening conditions (r = 0.70; P

Late leaf spot (LLS), caused by Phaeoisariopsis personata, is an important foliar fungal disease of groundnut (Arachis hypogaea L.), which causes significant economic losses globally to the crop. Inheritance of resistance to LLS disease was studied in three crosses and their reciprocals involving two resistant interspecific derivatives and a susceptible cultivar to refine strategy for LLS resistance breeding. The traits associated with LLS resistance, measured both in the field and under controlled conditions were studied following generation mean analysis. Results suggested that resistance to LLS is controlled by a combination of both, nuclear and maternal gene effects. Among nuclear gene effects, additive effect controlled majority of the variation. In JL 24 × ICG 11337 cross and its reciprocal only additive effects were important, while in JL 24 × ICG 13919 cross and its reciprocal, both additive and dominance effects contributed to the variation. Among digenic epistatic effects, additive × dominance interactions were significant. Additive–maternal effects were significant in both the crosses, while dominance–maternal effects also contributed to the variation in the crosses between the parents, JL 24 and ICG 13919. Due to significant contribution of additive effects of both nuclear and maternal inheritance to resistance to LLS, the parent, ICG 11337 would be a good donor in breeding programs. It would be worthwhile to use the resistance donor as female parent to tap maternal effects of resistance to LLS. Disease score is the best selection criterion in the field for use in breeding programs because of its high heritability and ease in measurement.

Botrytis grey mould (BGM), caused by the fungus Botrytis cinerea Pers. ex Fr., is an important disease of chickpea causing economic losses across the world in chickpea-growing regions. There are no available resistance sources in cultivated chickpea against this disease. Cicer echinospermum and C. reticulatum, the only two compatible annual wild species, have been reported to have resistance to BGM. Hence, interspecific populations were developed with susceptible cultivars as female parents and C. echinospermum accession IG 73 074 and C. reticulatum accession IG 72 937 as the pollen donors to transfer and assess the nature of genetic control for BGM. Screening the progeny indicated that resistance to BGM was controlled by a single additive gene/allele (bgmr1cr and bgmr1ce), which can be introgressed through a backcross breeding programme.