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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.

Iron deficiency chlorosis is an important abiotic stress affecting groundnut production worldwide in calcareous and alkaline soils with a pH of 7.5–8.5. To identify genomic regions controlling iron deficiency chlorosis resistance in groundnut, the recombinant inbred line population from the cross TAG 24 × ICGV 86031 was evaluated for associated traits like visual chlorosis rating and SPAD chlorophyll meter reading across three crop growth stages for two consecutive years. Thirty-two QTLs were identified for visual chlorosis rating (3.9%–31.8% phenotypic variance explained [PVE]) and SPAD chlorophyll meter reading [3.8%–11% PVE] across three stages over 2 years. This is the first report of identification of QTLs for iron deficiency chlorosis resistance- associated traits in groundnut. Three major QTLs (>10% PVE) were identified at severe stage, while majority of other QTLs were having small effects. Interestingly, two major QTLs for visual chlorosis rating at 60 days (2013) and 90 days (2014) were located at same position on LG AhXIII. The identified QTLs/markers after validation across diverse genetic material could be used in genomics-assisted breeding.

Pearl millet breeding programs can use this heterotic group information on seed and restorer parents to generate new series of pearl millet hybrids having higher yields than the existing hybrids. Five hundred and eighty hybrid parents, 320 R- and 260 B-lines, derived from 6 pearl millet breeding programs in India, genotyped following RAD-GBS (about 0.9 million SNPs) clustered into 12 R- and 7 B-line groups. With few exceptions, hybrid parents of all the breeding programs were found distributed across all the marker-based groups suggesting good diversity in these programs. Three hundred and twenty hybrids generated using 37 (22 R and 15 B) representative parents, evaluated for grain yield at four locations in India, showed significant differences in yield, heterosis, and combining ability. Across all the hybrids, mean mid- and better-parent heterosis for grain yield was 84.0% and 60.5%, respectively. Groups G12 B × G12 R and G10 B × G12 R had highest heterosis of about 10% over best check hybrid Pioneer 86M86. The parents involved in heterotic hybrids were mainly from the groups G4R, G10B, G12B, G12R, and G13B. Based on the heterotic performance and combining ability of groups, 2 B-line (HGB-1 and HGB-2) and 2 R-line (HGR-1 and HGR-2) heterotic groups were identified. Hybrids from HGB-1 × HGR-1 and HGB-2 × HGR-1 showed grain yield heterosis of 10.6 and 9.3%, respectively, over best hybrid check. Results indicated that parental groups can be formed first by molecular markers, which may not predict the best hybrid combination, but it can reveal a practical value of assigning existing and new hybrid pearl millet parental lines into heterotic groups to develop high-yielding hybrids from the different heterotic groups.

Indian dill seed (Anethum sowa Roxb. ex Fleming) is an important member of family Apiaceae. It is a significant seed spice having many medicinal properties. But, this aromatic herb is still orphan from breeding and crop improvement perspective as no serious attention has been given by breeders. To swift the breeding program, molecular markers play the main role. But due to the paucity of markers, breeding is slower in dill seed. Therefore, an attempt was made to develop the genomic SSR markers in dill seed through next-generation sequencing. A total of 2119.51 Mbp of raw data were generated on the Miseq NGS platform during survey sequencing. In 2,25,956 contigs created by Spades assembler, a total 48,951 repeat motifs were identified. A set of 20,294 primer pairs (dimer to hexamer repeats) were produced. Among detected repeat motifs, 48.89% was mononucleotides. Of 12 primers, 10 (83%) primers could be successfully amplified in dill seed and produced 11 amplicons. During cross-genera amplification of markers, 9 out of 10 primers could be successfully amplified in related genera. Developed markers can also be used to initiate the molecular breeding program, association mapping and to assess the evolutionary relationship among seed spices. Keywords: Anethum, Seed spices, SSR, Transferability

Cytoplasmic male sterility(CMS), a maternally inherited trait, provides a promising means to harness yield gains associated with hybrid vigor. In pigeonpea [Cajanus cajan (L.) Huth], nine types of sterility‐inducing cytoplasm have been reported, of which A2 and A4 have been successfully deployed in hybrid breeding. Unfortunately, molecular mechanism of the CMS trait is poorly understood because of limited research invested. More recently, an association between a mitochondrial gene (nad7) and A4‐CMS has been demonstrated in pigeonpea; however, the mechanism underlying A2‐CMS still remains obscure. The current investigation aimed to analyze the differences in A2‐CMS line (ICPL 88039A) and its isogenic maintainer line (ICPL 88039B) at transcriptome level using next‐generation sequencing. Gene expression profiling uncovered a set of 505 genes that showed altered expression in response to CMS, of which, 412 genes were upregulated while 93 were downregulated in the fertile maintainer line vs. the CMS line. Further, gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and protein–protein interaction (PPI) network analyses revealed association of CMS in pigeonpea with four major pathways: glucose and lipid metabolism, ATP production, pollen development and pollen tube growth, and reactive oxygen species (ROS) scavenging. Patterns of digital gene expression were confirmed by quantitative real‐time polymerase chain reaction (qRT‐PCR) of six candidate genes. This study elucidates candidate genes and metabolic pathways having potential associations with pollen development and male sterility in pigeonpea A2‐CMS. New insights on molecular mechanism of CMS trait in pigeonpea will be helpful to accelerate heterosis utilization for enhancing productivity gains in pigeonpea.

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

Exploitation of hybrid vigor using CMS technology has delivered nearly 50% yield gain in pigeonpea. Among various sterility-inducing cytoplasms (A1–A9) reported so far in pigeonpea, A2 and A4 are the two major sources that facilitate hybrid seed production. Recent evidence suggests involvement of micro RNA in vast array of biological processes including plant reproductive development. In pigeonpea, information about the miRNAs is insufficient. In view of this, we sequenced six small RNA libraries of CMS line UPAS 120A and isogenic fertile line UPAS 120B using Illumina technology. Results revealed 316 miRNAs including 248 known and 68 novel types. A total of 637 gene targets were predicted for known miRNAs, while 324 genes were associated with novel miRNAs. Degradome analysis revealed 77 gene targets of predicted miRNAs, which included a variety of transcription factors playing key roles in plant reproduction such as F-box family proteins, apetala 2, auxin response factors, ethylene-responsive factors, homeodomain-leucine zipper proteins etc. Differential expression of both known and novel miRNAs implied roles for both conserved as well as species-specific players. We also obtained several miRNA families such as miR156, miR159, miR167 that are known to influence crucial aspects of plant fertility. Gene ontology and pathway level analyses of the target genes showed their possible implications for crucial events during male reproductive development such as tapetal degeneration, pollen wall formation, retrograde signaling etc. To the best of our knowledge, present study is first to combine deep sequencing of small RNA and degradome for elucidating the role of miRNAs in flower and male reproductive development in pigeonpea.

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.

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.

The present investigation was performed to assess genetic divergence and heterosis prediction in hybrid parents of pearl millet [Pennisetum glaucum (L.) R Br.] using simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers. Using 56 SSR loci, 412 alleles were detected in 147 lines with an average of 7.36 alleles per locus, and 75,007 SNP loci were detected in 117 lines. Both SSR- and SNP-based clustering and structure analysis partitioned all maintainer (B) and restorer (R) lines into two clear-cut separate groups, indicating the existence of two diverse gene pools, each representing the seed and restorer parents in pearl millet. Results of analysis of molecular variance and principal coordinate analysis also showed significant diversity between B and R lines. The correlation between parental genetic distances estimated based on SSRs and SNPs was high and significant (r = 0.58, p < .01). Similar clustering pattern of hybrid parents was observed with both marker systems, although the cost of genotyping was 41% less with SNPs than with SSRs, and the ratio of loci detected with SNPs was much higher (1:364 SSR/SNP), hence the use of SNPs is indicated over SSRs for germplasm characterization. A set of 136 hybrids (including all B × B, R × R, and B × R crosses) generated crossing 17 hybrid parents (nine B lines and eight R lines) in half diallel (without reciprocal) fashion, and evaluation at two locations revealed that the correlation between genetic distance and better parent heterosis for grain yield was moderate, positive, and significant (with SSR, 0.33, p < .01; with SNP, 0.35, p < .01), hence both SSRs and SNPs were found comparable in results for heterosis prediction.

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.

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.

Fusarium wilt (FW) is one of the most important biotic stresses causing yield losses in pigeonpea. Genetic improvement of pigeonpea through genomics-assisted breeding (GAB) is an economically feasible option for the development of high yielding FW resistant genotypes. In this context, two recombinant inbred lines (RILs) (ICPB 2049 × ICPL 99050 designated as PRIL_A and ICPL 20096 × ICPL 332 designated as PRIL_B) and one F2 (ICPL 85063 × ICPL 87119) populations were used for the development of high density genetic maps. Genotyping-by-sequencing (GBS) approach was used to identify and genotype SNPs in three mapping populations. As a result, three high density genetic maps with 964, 1101 and 557 SNPs with an average marker distance of 1.16, 0.84 and 2.60 cM were developed in PRIL_A, PRIL_B and F2, respectively. Based on the multi-location and multi-year phenotypic data of FW resistance a total of 14 quantitative trait loci (QTLs) including six major QTLs explaining >10% phenotypic variance explained (PVE) were identified. Comparative analysis across the populations has revealed three important QTLs (qFW11.1, qFW11.2 and qFW11.3) with upto 56.45% PVE for FW resistance. This is the first report of QTL mapping for FW resistance in pigeonpea and identified genomic region could be utilized in GAB.

Successful management and utilization of increasingly large genomic datasets is essential for breeding programs to increase genetic gain and accelerate cultivar development. To help with data management and storage, we developed a sorghum Practical Haplotype Graph (PHG) pangenome database that stores all identified haplotypes and variant information for a given set of individuals. We developed two PHGs in sorghum, one with 24 individuals and another with 398 individuals, that reflect the diversity across genic regions of the sorghum genome. 24 founders of the Chibas sorghum breeding program were sequenced at low coverage (0.01x) and processed through the PHG to identify genome-wide variants. The PHG called SNPs with only 5.9% error at 0.01x coverage - only 3% lower than its accuracy when calling SNPs from 8x coverage sequence. Additionally, 207 progeny from the Chibas genomic selection (GS) training population were sequenced and processed through the PHG. Missing genotypes in the progeny were imputed from the parental haplotypes available in the PHG and used for genomic prediction. Mean prediction accuracies with PHG SNP calls range from 0.57-0.73 for different traits, and are similar to prediction accuracies obtained with genotyping-by-sequencing (GBS) or markers from sequencing targeted amplicons (rhAmpSeq). This study provides a proof of concept for using a sorghum PHG to call and impute SNPs from low-coverage sequence data and also shows that the PHG can unify genotype calls from different sequencing platforms. By reducing the amount of input sequence needed, the PHG has the potential to decrease the cost of genotyping for genomic selection, making GS more feasible and facilitating larger breeding populations that can capture maximum recombination. Our results demonstrate that the PHG is a useful research and breeding tool that can maintain variant information from a diverse group of taxa, store sequence data in a condensed but readily accessible format, unify genotypes from different genotyping methods, and provide a cost-effective option for genomic selection for any species.

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.

International audience; We report a map of 4.97 million single-nucleotide polymorphisms of the chickpea from whole-genome resequencing of 429 lines sampled from 45 countries. We identified 122 candidate regions with 204 genes under selection during chickpea breeding. Our data suggest the Eastern Mediterranean as the primary center of origin and migration route of chickpea from the Mediterranean/Fertile Crescent to Central Asia, and probably in parallel from Central Asia to East Africa (Ethiopia) and South Asia (India). Genome-wide association studies identified 262 markers and several candidate genes for 13 traits. Our study establishes a foundation for large-scale characterization of germplasm and population genomics, and a resource for trait dissection, accelerating genetic gains in future chickpea breeding.

This study was conducted to dissect the genetic basis and to explore the candidate genes underlying one of the important genomic regions on an SBI-10 long arm (L), governing the complex stay-green trait contributing to post-flowering drought-tolerance in sorghum. A fine-mapping population was developed from an introgression line cross&mdash, RSG04008-6 (stay-green) &times, J2614-11 (moderately senescent). The fine-mapping population with 1894 F2 was genotyped with eight SSRs and a set of 152 recombinants was identified, advanced to the F4 generation, field evaluated with three replications over 2 seasons, and genotyped with the GBS approach. A high-resolution linkage map was developed for SBI-10L using 260 genotyping by sequencing&mdash, Single Nucleotide Polymorphism (GBS&ndash, SNPs). Using the best linear unpredicted means (BLUPs) of the percent green leaf area (%GL) traits and the GBS-based SNPs, we identified seven quantitative trait loci (QTL) clusters and single gene, mostly involved in drought-tolerance, for each QTL cluster, viz., AP2/ERF transcription factor family (Sobic.010G202700), NBS-LRR protein (Sobic.010G205600), ankyrin-repeat protein (Sobic.010G205800), senescence-associated protein (Sobic.010G270300), WD40 (Sobic.010G205900), CPK1 adapter protein (Sobic.010G264400), LEA2 protein (Sobic.010G259200) and an expressed protein (Sobic.010G201100). The target genomic region was thus delimited from 15 Mb to 8 genes co-localized with QTL clusters, and validated using quantitative real-time (qRT)&ndash, PCR.

With high global demand, seeds and gum of cluster bean are an essential raw material for various industries. Worldwide the low yield and productivity of guar (Cyamopsis tetragonoloba) create a large gap between demand and supply of guar. Therefore, to upsurge guar production, there is a need to improve the guar at genetic level. The genetic improvement of cluster bean is slower due to insufficient genomic resources, co-dominant marker system especially simple sequence repeats (SSRs) and inadequate information on the variability of germplasm. For development of microsatellite markers in cluster bean, DNA survey sequencing was carried out using the Miseq NGS system. DNA sequencing generated 73,934 sequences which harboured microsatellite repeat sequences. Successfully, a total of 15,399 marker-pairs were designed. The amplicon size ranged between 101–385 base-pairs. To validate the primers and to analyse the diversity in released varieties and germplasm of cluster bean, successfully amplifiable 21 primers pairs were used. With a mean of 2.05 alleles per primers, 21 bands were detected. The polymorphism information content (PIC) for polymorphic markers fluctuated between 0.04 - 0.67 (mean = 0.3). With the average dissimilarity coefficient of 0.11, four clusters were noticed with NJ analysis. The grouping pattern of genotypes indicated a low genetic variability in the guar gene pool. The results of this study suggested that instead of re-circulation of parental lines, hybrid breeding using diverse parents followed by selection should be performed for genetic improvement of cluster bean. Keywords: Cluster bean, Diversity, DNA marker, NGS, SSR

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.

Chickpea (Cicer arietinum L.), a cool-season legume, is increasingly affected by heat-stress at reproductive stage due to changes in global climatic conditions and cropping systems. Identifying quantitative trait loci (QTLs) for heat tolerance may facilitate breeding for heat tolerant varieties. The present study was aimed at identifying QTLs associated with heat tolerance in chickpea using 292 F8-9 recombinant inbred lines (RILs) developed from the cross ICC 4567 (heat sensitive) &times, ICC 15614 (heat tolerant). Phenotyping of RILs was undertaken for two heat-stress (late sown) and one non-stress (normal sown) environments. A genetic map spanning 529.11 cM and comprising 271 genotyping by sequencing (GBS) based single nucleotide polymorphism (SNP) markers was constructed. Composite interval mapping (CIM) analysis revealed two consistent genomic regions harbouring four QTLs each on CaLG05 and CaLG06. Four major QTLs for number of filled pods per plot (FPod), total number of seeds per plot (TS), grain yield per plot (GY) and % pod setting (%PodSet), located in the CaLG05 genomic region, were found to have cumulative phenotypic variation of above 50%. Nineteen pairs of epistatic QTLs showed significant epistatic effect, and non-significant QTL &times, environment interaction effect, except for harvest index (HI) and biomass (BM). A total of 25 putative candidate genes for heat-stress were identified in the two major genomic regions. This is the first report on QTLs for heat-stress response in chickpea. The markers linked to the above mentioned four major QTLs can facilitate marker-assisted breeding for heat tolerance in chickpea.

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.

Chickpea is the most important pulse crop globally after dry beans. Climate change and increased cropping intensity are forcing chickpea cultivation to relatively higher temperature environments. To assess the genetic variability and identify heat responsive traits, a set of 296 F8–9 recombinant inbred lines (RILs) of the cross ICC 4567 (heat sensitive) × ICC 15614 (heat tolerant) was evaluated under field conditions at ICRISAT, Patancheru, India. The experiment was conducted in an alpha lattice design with three replications during the summer seasons of 2013 and 2014 (heat stress environments, average temperature 35 °C and above), and post-rainy season of 2013 (non-stress environment, max. temperature below 30 °C). A two-fold variation for number of filled pods (FPod), total number of seeds (TS), harvest index (HI), percent pod setting (%PodSet) and grain yield (GY) was observed in the RILs under stress environments compared to non-stress environment. A yield penalty ranging from 22.26% (summer 2013) to 33.30% (summer 2014) was recorded in stress environments. Seed mass measured as 100-seed weight (HSW) was the least affected (6 and 7% reduction) trait, while %PodSet was the most affected (45.86 and 44.31% reduction) trait by high temperatures. Mixed model analysis of variance revealed a high genotypic coefficient of variation (GCV) (23.29–30.22%), phenotypic coefficient of variation (PCV) (25.69–32.44%) along with high heritability (80.89–86.89%) for FPod, TS, %PodSet and GY across the heat stress environments. Correlation studies (r = 0.61–0.97) and principal component analysis (PCA) revealed a strong positive association among the traits GY, FPod, VS and %PodSet under stress environments. Path analysis results showed that TS was the major direct and FPod was the major indirect contributors to GY under heat stress environments. Therefore, the traits that are good indicators of high grain yield under heat stress can be used in indirect selection for developing heat tolerant chickpea cultivars. Moreover, the presence of large genetic variation for heat tolerance in the population may provide an opportunity to use the RILs in future-heat tolerance breeding programme in chickpea.

Yield under drought stress is a highly complex trait with large influence to even a minor fluctuation in the environmental conditions. Genomics-assisted breeding holds great promise for improving such complex traits more efficiently in less time, but requires markers associated with the trait of interest. In this context, a recombinant inbred line mapping population (TAG 24 × ICGV 86031) was used to identify markers associated with quantitative trait loci (QTLs) for yield and yield related traits at two important locations of West Africa under well watered and water stress conditions. Among the traits analyzed under WS condition, the harvest index (HI) and the haulm yield (HYLD) were positively correlated with the pod yield (PYLD) and showed intermediate broad sense heritability. QTL analysis using phenotyping and genotyping data resulted in identification of 52 QTLs. These QTLs had low phenotypic variance (

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.

Key message Analysis of phenotypic data for 20 drought tolerance traits in 1–7 seasons at 1–5 locations together with genetic mapping data for two mapping populations provided 9 QTL clusters of which one present on CaLG04 has a high potential to enhance drought tolerance in chickpea improvement. Abstract Chickpea (Cicer arietinum L.) is the second most important grain legume cultivated by resource poor farmers in the arid and semi-arid regions of the world. Drought is one of the major constraints leading up to 50 % production losses in chickpea. In order to dissect the complex nature of drought tolerance and to use genomics tools for enhancing yield of chickpea under drought conditions, two mapping populations—ICCRIL03 (ICC 4958 × ICC 1882) and ICCRIL04 (ICC 283 × ICC 8261) segregating for drought tolerance-related root traits were phenotyped for a total of 20 drought component traits in 1–7 seasons at 1–5 locations in India. Individual genetic maps comprising 241 loci and 168 loci for ICCRIL03 and ICCRIL04, respectively, and a consensus genetic map comprising 352 loci were constructed (http://cmap.icrisat.ac.in/cmap/sm/cp/varshney/). Analysis of extensive genotypic and precise phenotypic data revealed 45 robust main-effect QTLs (M-QTLs) explaining up to 58.20 % phenotypic variation and 973 epistatic QTLs (E-QTLs) explaining up to 92.19 % phenotypic variation for several target traits. Nine QTL clusters containing QTLs for several drought tolerance traits have been identified that can be targeted for molecular breeding. Among these clusters, one cluster harboring 48 % robust M-QTLs for 12 traits and explaining about 58.20 % phenotypic variation present on CaLG04 has been referred as “QTL-hotspot”. This genomic region contains seven SSR markers (ICCM0249, NCPGR127, TAA170, NCPGR21, TR11, GA24 and STMS11). Introgression of this region into elite cultivars is expected to enhance drought tolerance in chickpea. Electronic supplementary material The online version of this article (doi:10.1007/s00122-013-2230-6) contains supplementary material, which is available to authorized users.

Transgenic research using the DREB group of transcription factors has received much attention in developing drought-tolerant and climate-ready varieties of crop plants. While many reports have demonstrated increased tolerance to water deficits under laboratory and greenhouse conditions, only a few have tested possible effects under field conditions, with limited success in most cases. Here, we present evidence of a transgenic solution for enhanced drought tolerance in peanut (Arachis hypogaea L.), which is an important grain legume and a valuable cash crop for smallholder and resource-poor farmers occupying the largest portion of the farming systems in low income food deficit countries. The presence, integration, expression and inheritance of the transgene in advancing generations of the transgenic peanut plants were assessed using PCR, Southern blot, inverse-PCR, RT-PCR and q-PCR techniques. Four trials were conducted in various water stress regimes under varying vapour pressure deficits (VPDs), and drought tolerance was studied using various component traits of drought. A substantial yield improvement of up to 24 % in drought trials under field conditions was achieved across a wide range of stress intensities and was related to higher harvest indices (HIs). All transgenic events had significantly higher seed filling under drought and displayed 20–30 % lower pod yield reduction than their untransformed counterpart under drought stress. Two transgenic events showed yield advantage under drought stress that consistently had higher pod and seed yield than the untransformed parent under drought stress across all trials, without displaying any yield penalty under irrigated conditions.

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.

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.

Pigeonpea (Cajanus cajan), a tropical grain legume with low input requirements, is expected to continue to have an important role in supplying food and nutritional security in developing countries in Asia, Africa and the tropical Americas. From whole-genome resequencing of 292 Cajanus accessions encompassing breeding lines, landraces and wild species, we characterize genome-wide variation. On the basis of a scan for selective sweeps, we find several genomic regions that were likely targets of domestication and breeding. Using genome-wide association analysis, we identify associations between several candidate genes and agronomically important traits. Candidate genes for these traits in pigeonpea have sequence similarity to genes functionally characterized in other plants for flowering time control, seed development and pod dehiscence. Our findings will allow acceleration of genetic gains for key traits to improve yield and sustainability in pigeonpea.

Sterility mosaic disease (SMD) is one of the serious production constraints that may lead to complete yield loss in pigeonpea. Three mapping populations including two recombinant inbred lines and one F2, were used for phenotyping for SMD resistance at two locations in three different years. Genotyping-by-sequencing approach was used for simultaneous identification and genotyping of SNPs on above mentioned populations. In total, 212,464, 89,699 and 64,798 SNPs were identified in ICPL 20096 × ICPL 332 (PRIL_B), ICPL 20097 × ICP 8863 (PRIL_C) and ICP 8863 × ICPL 87119 (F2) respectively. By using high-quality SNPs, genetic maps were developed for PRIL_B (1,101 SNPs; 921.21 cM), PRIL_C (484 SNPs; 798.25 cM) and F2 (996 SNPs; 1,597.30 cM) populations. The average inter marker distance on these maps varied from 0.84 cM to 1.65 cM, which was lowest in all genetic mapping studies in pigeonpea. Composite interval mapping based QTL analysis identified a total of 10 QTLs including three major QTLs across the three populations. The phenotypic variance of the identified QTLs ranged from 3.6 to 34.3%. One candidate genomic region identified on CcLG11 seems to be promising QTL for molecular breeding in developing superior lines with enhanced resistance to SMD.

SUMMARYPigeonpea is an important legume crop of the semi-arid tropics. In India, pigeonpea is mostly grown in areas prone to waterlogging, resulting in major production losses. It is imperative to identify genotypes that show tolerance at critical crop growth stages to prevent these losses. A selection of 272 diverse pigeonpea accessions was evaluated for seed submergence tolerance for different durations (0, 120, 144, 168 and 192 h) under in vitro conditions in the laboratory. All genotypes exhibited high (0·79–0·98) survival rates for up to 120 h of submergence. After 192 h of submergence, the hybrids as a group exhibited significantly higher survival rates (0·79) than the germplasm (0·71), elite breeding lines (0·68) and commercial varieties (0·58). Ninety-six genotypes representing the phenotypic variation observed during laboratory screening were further evaluated for waterlogging tolerance at the early seedling stage using pots, and survival rates were recorded for 8 days after completion of the stress treatment. Forty-nine of these 96 genotypes, representing the phenotypic variation for waterlogging tolerance, were chosen in order to evaluate their performance under natural field conditions. The following cultivated varieties and hybrids were identified as tolerant after three levels of testing (in vitro, in pots and in the field): ICPH 2431, ICPH 2740, ICPH 2671, ICPH 4187, MAL 9, LRG 30, Maruti, ICPL 20128, ICPL 332, ICPL 20237, ICPL 20238, Asha and MAL 15. These materials can be used as sources of waterlogging tolerance in breeding programmes.

Pigeonpea (Cajanus cajan L.) is an important food legume crop of rainfed agriculture. Owing to exposure of the crop to a number of biotic and abiotic stresses, the crop productivity has remained stagnant for almost last five decades at ca. 750 kg/ha. The availability of a cytoplasmic male sterility (CMS) system has facilitated the development and release of hybrids which are expected to enhance the productivity of pigeonpea. Recent advances in genomics and molecular breeding such as marker-assisted selection (MAS) offer the possibility to accelerate hybrid breeding. Molecular markers and genetic maps are pre-requisites for deploying MAS in breeding. However, in the case of pigeonpea, only one inter- and two intra-specific genetic maps are available so far. Here, four new intra-specific genetic maps comprising 59–140 simple sequence repeat (SSR) loci with map lengths ranging from 586.9 to 881.6 cM have been constructed. Using these four genetic maps together with two recently published intra-specific genetic maps, a consensus map was constructed, comprising of 339 SSR loci spanning a distance of 1,059 cM. Furthermore, quantitative trait loci (QTL) analysis for fertility restoration (Rf) conducted in three mapping populations identified four major QTLs explaining phenotypic variances up to 24 %. To the best of our knowledge, this is the first report on construction of a consensus genetic map in pigeonpea and on the identification of QTLs for fertility restoration. The developed consensus genetic map should serve as a reference for developing new genetic maps as well as correlating with the physical map in pigeonpea to be developed in near future. The availability of more informative markers in the bins harbouring QTLs for sterility mosaic disease (SMD) and Rf will facilitate the selection of the most suitable markers for genetic analysis and molecular breeding applications in pigeonpea. Electronic supplementary material The online version of this article (doi:10.1007/s00122-012-1916-5) contains supplementary material, which is available to authorized users.

Sorghum [Sorghum bicolor (L.) Moench] is a very important crop in the arid and semi-arid tropics of India and African subcontinent. In the process of release of new cultivars using multi-location data major emphasis is being given on the superiority of the new cultivars over the ruling cultivars, while very less importance is being given on the genotype × environment interaction (GEI). In the present study, performance of ten Indian hybrids over 12 locations across the rainy seasons of 2008 and 2009 was investigated using GGE biplot analysis. Location attributed higher proportion of the variation in the data (59.3–89.9%), while genotype contributed only 3.9–16.8% of total variation. Genotype × location interaction contributed 5.8–25.7% of total variation. We could identify superior hybrids for grain yield, fodder yield and for harvest index using biplot graphical approach effectively. Majority of the testing locations were highly correlated. ‘Which-won-where’ study partitioned the testing locations into three mega-environments: first with eight locations with SPH 1606/1609 as the winning genotypes; second mega-environment encompassed three locations with SPH 1596 as the winning genotype, and last mega-environment represented by only one location with SPH 1603 as the winning genotype. This clearly indicates that though the testing is being conducted in many locations, similar conclusions can be drawn from one or two representatives of each mega-environment. We did not observe any correlation of these mega-environments to their geographical locations. Existence of extensive crossover GEI clearly suggests that efforts are necessary to identify location-specific genotypes over multi-year and -location data for release of hybrids and varieties rather focusing on overall performance of the entries.

Chickpea is the third most important pulse crop worldwide. Changes in cropping system that necessitate late planting, scope for expansion in rice fallows and the global warming are pushing chickpeas to relatively warmer growing environment. Such changes demand identification of varieties resilient to warmer temperature. Therefore, the reference collection of chickpea germplasm, defined based on molecular characterization of global composite collection, was screened for high temperature tolerance at two locations in India (Patancheru and Kanpur) by delayed sowing and synchronizing the reproductive phase of the crop with the occurrence of higher temperatures ( ≥ 35°C). A heat tolerance index (HTI) was calculated using a multiple regression approach where grain yield under heat stress is considered as a function of yield potential and time to 50% flowering. There were large and significant variations for HTI, phenology, yield and yield components at both the locations. There were highly significant genotypic effects and equally significant G × E interactions for all the traits studied. A cluster analysis of the HTI of the two locations yielded five cluster groups as stable tolerant (n = 18), tolerant only at Patancheru (n = 34), tolerant only at Kanpur (n = 23), moderately tolerant (n = 120) and stable sensitive (n = 82). The pod number per plant and the harvest index explained ≥ 60% of the variation in seed yield and ≥ 49% of HTI at Kanpur and ≥ 80% of the seed yield and ≥ 35% of HTI at Patancheru, indicating that partitioning as a consequence of poor pod set is the most affected trait under heat stress. A large number of heat-tolerant genotypes also happened to be drought tolerant.

Axiom Cajanus SNP array revealed genetic architecture and temporal diversity in pigeonpea varieties. As one of the major outputs of next‐generation sequencing (NGS), a large number of genome‐wide single‐nucleotide polymorphisms (SNPs) have been developed in pigeonpea [Cajanus cajan (L.) Huth.]. However, SNPs require a genotyping platform or assay to be used in different evolutionary studies or in crop improvement programs. Therefore, we developed an Axiom Cajanus SNP array with 56K SNPs uniformly distributed across the genome and assessed its utility in a genetic diversity study. From the whole‐genome resequencing (WGRS) data on 104 pigeonpea lines, ∼2 million sequence variations (SNPs and insertion–deletions [InDels]) were identified, from which a subset of 56,512 unique and informative sequence variations were selected to develop the array. The Axiom Cajanus SNP array developed was used for genotyping 103 pigeonpea lines encompassing 63 cultivars released between 1960 and 2014 and 40 breeding, germplasm, and founder lines. Genotyping data thus generated on 103 pigeonpea lines provided 51,201 polymorphic SNPs and InDels. Genetic diversity analysis provided in‐depth insights into the genetic architecture and trends in temporal diversity in pigeonpea cultivars. Therefore, the continuous use of the high‐density Axiom Cajanus SNP array developed will accelerate high‐resolution trait mapping, marker‐assisted breeding, and genomic selection efforts in pigeonpea.

Pearl millet is a climate-resilient nutritious crop requiring low inputs and is capable of giving economic returns in marginal agro-ecologies. In this study, we report large-effect iron (Fe) and zinc (Zn) content quantitative trait loci (QTLs) using diversity array technology (DArT) and simple sequence repeats (SSRs) markers to generate a genetic linkage map using 317 recombinant inbred line (RIL) population derived from the (ICMS 8511-S1-17-2-1-1-B-P03 × AIMP 92901-S1-183-2-2-B-08) cross. The base map [seven linkage groups (LGs)] of 196 loci was 964.2 cM in length (Haldane). AIMP 92901-S1-183-2-2-B-08 is an Iniadi line with high grain Fe and Zn, tracing its origin to the Togolese Republic, West Africa. The content of grain Fe in the RIL population ranged between 20 and 131 ppm (parts per million), and that of Zn from 18 to 110 ppm. QTL analysis revealed a large number of QTLs for high grain iron (Fe) and zinc (Zn) content. A total of 19 QTLs for Fe and Zn were detected, of which 11 were for Fe and eight were for Zn. The portion of the observed phenotypic variance explained by different QTLs for grain Fe and Zn content varied from 9.0 to 31.9% (cumulative 74%) and from 9.4 to 30.4% (cumulative 65%), respectively. Three large-effect QTLs for both minerals were co-mapped in this population, one on LG1 and two on LG7. The favorable QTL alleles of both mineral micronutrients were contributed by the male parent (AIMP 92901-deriv-08). Three putative epistasis interactions were observed for Fe content, while a single digenic interaction was found for Zn content. The reported QTLs may be useful in marker-assisted selection (MAS) programs, in genomic selection (GS) breeding pipelines for seed and restorer parents, and in population improvement programs for pearl millet.

Knowledge of current genetic diversity and mating systems of crop wild relatives (CWR) in the Fertile Crescent is important in crop genetic improvement, because western agriculture began in the area after the cold-dry period known as Younger Dryas about 12,000 years ago and these species are also wild genepools of the world's most important food crops. Wild pea (Pisum sativum subsp. elatius) is an important source of genetic diversity for further pea crop improvement harbouring traits useful in climate change context. The genetic structure was assessed on 187 individuals of Pisum sativum subsp. elatius from fourteen populations collected in the northern part of the Fertile Crescent using 18,397 genome wide single nucleotide polymorphism DARTseq markers. AMOVA showed that 63% of the allelic variation was distributed between populations and 19% between individuals within populations. Four populations were found to contain admixed individuals. The observed heterozygosity ranged between 0.99 to 6.26% with estimated self-pollination rate between 47 to 90%. Genetic distances of wild pea populations were correlated with geographic but not environmental (climatic) distances and support a mixed mating system with predominant self-pollination. Niche modelling with future climatic projections showed a local decline in habitats suitable for wild pea, making a strong case for further collection and ex situ conservation.