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Sheath blight is an emerging disease of rice that appears in rice production areas worldwide. A total of 294 O. nivara accessions along with susceptible check PR114, the cultivated rice, were screened against sheath blight under field conditions for three consecutive years. Based on screening, 15 accessions were identified that showed moderate resistance reaction to sheath blight across the years. However, none of the accession showed highly resistant reaction. Sheath blight resistance was found to be quantitative controlled based on near normal distribution of lesion length. These 15 accessions further showed same level of resistance in detached tiller culture method and are proposed as the candidate donors for resistance to sheath blight, to be used in rice breeding programme. Further Multi locus-GWAS implemented using the 3VmrMLM model in 294 O. nivara accessions using 22,261 SNPs identified 11 marker-trait associations (MTAs) on 8 different chromosomes with the LOD score ranging from 3.34 to 20.58, while 10 out of 11 significant showed significant statistical difference based on Kruskal–Wallis test. Based on the LD decay in the panel, an interval of ± 300 kb of each significant MTA was investigated to identify candidate genes governing resistance to sheath blight. Among 11 QTL regions, a total of 19 candidate genes were found to be differentially expressed in response to the sheath blight pathogen based on in-depth in silico analysis, including those encoding lignin biosynthesis proteins, calcineurin B, thaumatin proteins, protein kinase domains, NBS-LRR domains, and cytochrome P450 oxidoreductases. The study highlighted 15 sheath blight resistant donors along with 10 QTL regions and 19 candidate genes that will provide a platform for understanding genetic basis of sheath blight resistance in rice. [ABSTRACT FROM AUTHOR]

Heat stress during reproductive stages has been leading to significant yield losses in chickpea (Cicer arietinum L.). With an aim of identifying the genomic regions or QTLs responsible for heat tolerance, 187 F8 recombinant inbred lines (RILs) derived from the cross GPF 2 (heat tolerant) × ILWC 292 (heat sensitive) were evaluated under late-sown irrigated (January-May) and timely-sown irrigated environments (November-April) at Ludhiana and Faridkot in Punjab, India for 13 heat tolerance related traits. The pooled ANOVA for both locations for the traits namely days to germination (DG), days to flowering initiation (DFI), days to 50% flowering (DFF), days to 100% flowering (DHF), plant height (PH), pods per plant (NPP), biomass (BIO), grain yield (YLD), 100-seed weight (HSW), harvest index (HI), membrane permeability index (MPI), relative leaf water content (RLWC) and pollen viability (PV)) showed a highly significant difference in RILs. The phenotyping data coupled with the genetic map comprising of 1365 ddRAD-Seq based SNP markers were used for identifying the QTLs for heat tolerance. Composite interval mapping provided a total of 28 and 23 QTLs, respectively at Ludhiana and Faridkot locations. Of these, 13 consensus QTLs for DG, DFI, DFF, DHF, PH, YLD, and MPI have been identified at both locations. Four QTL clusters containing QTLs for multiple traits were identified on the same genomic region at both locations. Stable QTLs for days to flowering can be one of the major factors for providing heat tolerance as early flowering has an advantage of more seed setting due to a comparatively longer reproductive period. Identified QTLs can be used in genomics-assisted breeding to develop heat stress-tolerant high yielding chickpea cultivars. [ABSTRACT FROM AUTHOR]

The gene-for-gene relationship of host–pathogen interaction explained by H. H. Flor in mid of the 20th century set a milestone in understanding the biochemical and genetic basis of plant diseases and several components involved in plant–pathogen interactions. It highlighted the importance of accomplishing differential sets and understanding the pathogen population structure, it further led to the identification and cloning of several resistance (R) genes in plants. These R genes have been deployed and altered for fighting against diseases in a large number of crops using various conventional approaches and biotechnological tools. Identification of R genes and their corresponding Avr genes in many cases played a significant role in understanding of R-Avr gene interactions. Rapid cloning of R genes and editing of susceptible R genes are the other avenues that have broadened the horizon of utilizing R genes in crop improvement programmes. Further, combining R genes with quantitative disease resistance genes has paved the way to develop durable resistance in cultivars. The recent advances in genetics, genomics, bioinformatics and other OMICS tools are now providing greater prospects for deeper understanding of host–pathogen interaction. [ABSTRACT FROM AUTHOR]

Ascochyta blight (AB) and botrytis grey mould (BGM) are the most devastating fungal diseases of chickpea worldwide. The wild relative of chickpea, C. reticulatum acc. ILWC 292 was found resistant to BGM whereas, GPF2 (Cicer arietinum L.) is resistant to AB. A total of 187 F8 Recombinant Inbred Lines (RILs) developed from an inter-specific cross of GPF2 × C. reticulatum acc. ILWC 292 were used to identify quantitative trait loci (QTLs) responsible for resistance to AB and BGM. RILs along with parents were evaluated under artificial epiphytotic field/laboratory conditions for two years. Highly significant differences (P < 0.001) were observed for reaction to both pathogens in both years. Parents and RILs were genotyped-bysequencing to identify genome wide single nucleotide polymorphism (SNPs). A total of 1365 filtered and parental polymorphic SNPs were used for linkage map construction, of which, 673 SNPs were arranged on eight linkage groups. Composite interval mapping revealed three QTLs for AB and four QTLs for BGM resistance. Out of which, two QTLs for AB and three QTLs for BGM were consistent in both years. These QTLs can be targeted for further fine mapping for deployment of resistance to AB and BGM in elite chickpea cultivars using marker-assisted-selection. [ABSTRACT FROM AUTHOR]

Breeding for insect resistant varieties has been central to the integrated pest management as it offers an ecologically viable approach agianst biotic constraints. Considerable progress has been made in the past to incorporate resistance to insect pests of rice using conventional breeding approaches. However the diversity in insect pest population, continuous selection of virulent biotypes, lack of resistance sources in cultivated rice (Oryza sativa and O. glaberrima) gene pool, want of efficient insect rearing and varietal screening protocols and inherently complex genetics of resistance further necessitates supplementation of conventional breeding techniques with advanced molecular approaches. Hence, alternative approaches like wide hybridization to introgress resistance from other species of Oryza, transgenic approach to deploy Bt cry, snowdrop lectin and other plant derived genes are being actively pursued. The increasingly identified, mapped, cloned and characterized quantitative trait loci and genes related to insect resistance traits in rice have provided a solid foundation for direct selection and varietal improvement through molecular breeding. Utilization of DNA-based markers provided additional impetus to efficiency and precision of conventional plant breeding via marker-assisted selection to successfully introgress several genes for resistance to insect pests of rice. RNA interference technology has offered another reliable tool in meeting the challenges imposed by crop insects by targeting the enzymes/proteins integral to various biological processes of crop insects. This review briefly discusses the current progress and future prospects in molecular breeding for enhanced varietal tolerance to insect pests of rice. [ABSTRACT FROM AUTHOR]

Considering the potentials of wild rice (Oryza spp.), as well as the need to enhance the yield potential of rice and to increase rice production to meet increasing demands, 1780 backcross inbred lines (BILs) were generated by crossing 70 accessions of six "AA" genome species: Oryza glaberrima Steud., Oryza barthii A. Chev., Oryza nivara Sharma & Shastry, Oryza rufpogon Griff., Oryza longistaminata A. Chev. & Roehr., and Oryza glumaepatula Steud. with two elite cultivars of Oryza sativa L. The wild species accessions were selected based on variation at the DNA markers and agromorphological traits. The BILs were generated by backcrossing F1s twice (thrice in some cases) to recipient parents, followed by continuous selfing and selection for the yield and yield component traits. The set of 1780 BC2F5 to BC2F10 BILs were evaluated in an augmented design over 3 yr. Based on ANOVA in augmented design, 108 agronomically superior BILs were selected and evaluated in randomized complete block design. Of the 108 BILs evaluated, 15 BILs showed >10% yield superiority over the recurrent parent, with spikelet per panicle and thousand-grain weight as most significant traits contributing to yield increase. Based on the contribution of donor accessions for the improvement of yield component traits, six accessions of O. glaberrima, one of O. barthii, two of O. nivara, two of O. rufpogon, and one each of O. longistaminata and O. glumaepatula were identified as potential donors that could be used more rigorously in transferring genes to cultivated rice. The BILs generated in the present study represents a reservoir of novel genetic variation. [ABSTRACT FROM AUTHOR]

Sheath blight of rice caused by Rhizoctonia solani Kuhn [teleomorph: Thanatephorus cucumeris (Frank) Donk] is a significant threat to rice cultivation, accounting for up to 50% yield losses. The present investigation demonstrates the early pathogenesis events and R. solani pre‐ and post‐penetration activities on moderately resistant (MR) and highly susceptible (HS) lines under field conditions. A pure culture of R. solani isolate (R1965) was inoculated inside the sheath at the maximum tillering stage for different time intervals (24, 48, 72 and 96 hpi). R. solani exhibited more profuse, dense, closely contact around surface grooves, lobate appressoria‐like structures and greater microsclerotia development on the HS line compared to the MR one. Using fluorescent, optical, and scanning electron microscopy, it was noticed for the first time that R. solani could intercept sheath papillae and employ them for attachment or penetration in two ways: (a) direct penetration by lobate or runner hyphae, appressorium and infection cushion and (b) indirect stomatal penetration. Assays using in vivo plant inoculation showed that disease lesion length was higher in the HS line than the MR line. Intraxylary hyphal colonization could be seen using microtomy to understand the cellular spatial dynamics of xylem colonization by R. solani. The penetration mechanism along with penetration hyphae of the R. solani inside HS rice lines describe in this paper for the first time using optical ultrastructure. These results supported for better understanding of host–pathogen interaction, penetration mechanism and colonization of R. solani in rice. [ABSTRACT FROM AUTHOR]

Highlights: [•] Generate a complete collection of RefSeqs for all 23 species of the genus. [•] Produce advanced mapping populations for functional and breeding studies. [•] Conserve the wild relatives of rice for future breeding and molecular applications. [Copyright &y& Elsevier]

Bacterial blight (BB), caused by Xanthomonas oryzae pv. oryzae, is a major disease of rice managed largely through the deployment of resistance genes. Xa38, a BB resistance gene identified from Oryza nivara acc. IRGC 81825, was mapped on chromosome 4L in a 38.4-kb region. The closely linked markers for this gene, identified earlier, were simple sequence repeat marker RM17499 and sequence-tagged site markers developed from loci Os04g53060 and Os04g53120. Marker Os04g53060 is dominant while the other two markers show smaller size differences difficult to resolve accurately on agarose gel. Based on gene annotation, three nucleotide binding site-leucine-rich repeat genes present in the target region were cloned from O. nivara and sequenced. One of the loci, LOC_Os04g53050, had a 48-base-pair deletion in O. nivara acc. IRGC 81825 compared to the cultivated rice. Primers were designed around the deletion and the resulting marker is codominant and easy to score in agarose gel. The newly designed marker co-segregated with Xa38, amplifying products of 269 bp in O. nivara and 317 bp in cultivated rice. This marker could be more useful for marker-assisted selection than ones reported earlier. [ABSTRACT FROM AUTHOR]

BACKGROUND RESULTS CONCLUSION Yellow mosaic disease (YMD) is the most devastating disease of soybean under north Indian conditions. A recombinant inbred line population derived from SL 958 (R) × AGS 456 (S) was used to map the genes imparting YMD resistance. Genotyping by sequencing (GBS) of 148 individuals and the parents was used to identify polymorphic SNPs in the population. These were used to generate linkage maps and subsequently map the QTL.A QTL, MYMIV 1‐1.1, was mapped onto chromosome 6. The QTL was mapped at a genetic distance of 114.31 cM, with likelihood ratio of 81.34 (LOD 17.68), explaining 33.80% of the variation for the trait, with an additive effect of 1.22. MYMIV 1‐1.1 was flanked by SNPs Gm06_12614920 explaining 33.80% of variation and Gm06_12887789 explaining 31.04% of the variation. The QTL region spanned for a total of 2.798 Mbp.The QTL was mapped in an approximately 4 cM region. Flanking SNPs can be developed into linked markers for effective marker‐assisted selection. Out of the genes in the QTL region, Glyma.06G161700 (Suppressor of Gene Silencing/SGS3) is the strongest contender for the resistance gene. This is the first study documenting GBS‐based mapping of YMD resistance in soybean. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Increasing seed oil content (SOC) is one of the important breeding objectives in canola quality Brassica napus, a second largest oil producing oilseed crop after soybean in the world. A fixed diversity stock of 200 canola quality genotypes, acquired from diverse geographical locations, was evaluated for SOC across environments. An association mapping panel was constituted and genotyped using genotype-by-sequencing. Significant variation was observed for genotypes, environment and genotype-by environment interaction in SOC. Best linear unbiased predictors (BLUPs) was used for genome-wide association study (GWAS) with 85,126 SNPs. A total of 14 SNPs on four chromosomes i.e., A03, A07, A09 and C05 was found significantly associated with SOC. Four SNPs (three on A07, one on A09) were significantly associated with SOC across the environments. Genomic region identified on chromosome A09 was previously reported to be associated with oleic acid content, a major component of SOC in B. napus. Novel SNPs associated with SOC were identified on chromosomes A03, A07 and C05. Candidate genes involved in regulation of lipid metabolism and biosynthesis were identified within confidence interval of SOC associated SNPs. It suggests complex mechanism due to the role of multiple direct and indirect genes governing the SOC in B. napus. A set of 15 genotypes having high oil content across the years and locations, were recommended for commercial breeding targeted to SOC improvement. This study provides insight for further improvement of SOC in B. napus through molecular breeding and marker assisted selection. [ABSTRACT FROM AUTHOR]

This research paper investigates the variability in seed oil content (SOC) in Indian mustard (Brassica juncea L.) under terminal heat stress (THS) conditions. A genetic stock of 488 genotypes of B. juncea was evaluated over two years and grouped into five classes based on the reduction in oil content under THS compared to normal sown crop. Based on heat susceptibility index (HSI), a diverse panel of 96 genotypes was selected and evaluated under THS. Twenty-two heat-tolerant donor genotypes were identified, including introgression lines derived from B. tournefortii, B. carinata and Erucastrum cardaminoides. This study is the first to report on marker–trait associations for SOC in B. juncea under THS using a GWAS approach. Furthermore, candidate genes associated with abiotic stress tolerance and lipid metabolism were identified near the significant SNPs, emphasizing their role in SOC regulation under stress. Notable candidate genes include BjuA003240 (encoding for alcohol-forming fatty acyl-CoA reductase), BjuA003242 (involving in lipid biosynthesis), BjuA003244 (associated with mitochondrial functions and stress tolerance), and BjuA003245 (related to MYB transcription factors regulating lipid biosynthesis). This study provides valuable insights into the genetic basis of SOC variation under THS in B. juncea, highlighting potential breeding targets for improved heat stress resilience in Indian mustard cultivation. [ABSTRACT FROM AUTHOR]

Drought is a major abiotic stress worldwide limiting chickpea yield drastically. Low heritability and high genotype × environment interactions make the trait-based breeding strategy an unreliable approach. This study was planned to identify the drought-tolerant lines by evaluating yield-based selection indices in a recombinant inbred line (RIL) population derived from an inter-specific cross between drought-tolerant genotype GPF 2 (Cicer arietinum L.) and drought-sensitive accession ILWC 292 (C. reticulatum) at two locations in India (Ludhiana and Faridkot). A total of six yield-based selection indices were calculated and significant variation was observed in the RILs and their parents for yield-based selection indices at both locations. A holistic approach across association analysis and principal component analysis identified drought tolerance index, mean productivity, geometric mean productivity and harmonic mean productivity as key selection indices, which could be used for indirect selection of drought-tolerant lines. Overall, on the basis of these approaches, a total of 15 promising RILs were identified for their use in chickpea breeding programme for developing drought-tolerant cultivars. [ABSTRACT FROM AUTHOR]

Introgression Lines (ILs) carrying alien genomic segments in the homozygous state may or may not be able to contribute positively to the phenotype on account of replacement of cultivated genome segment, however, the genetic elite in heterozygous condition can be attributed to the presence of both recipient and donor genome complements. Therefore, overdominance or pseudo‐overdominance effect at the heterozygous loci is anticipated. Set of 318 ILs, carrying several genomic segments from "A" genome donor wild species, were used for developing test hybrids with CMS line PMS17A. Of these, three hybrids observed significant yield advantage (>25%) over recurrent parents and checks. Parental ILs of these hybrids viz., IL326, IL901 and IL951 carried 5.62%, 2.52% introgression from Oryza rufipogon and 6.71% from Oryza nivara, respectively. These ILs were also crossed with their recurrent parent to develop introgression line hybrids (ILHs) to observe the contribution of the alien segment(s), in the homozygous and heterozygous state. The traits studied have higher mean value when genomic segments from wild species were in the heterozygous state as compared to the homozygous state. [ABSTRACT FROM AUTHOR]

Doubled haploid (DH) breeding is a powerful technique to ensure global food security via accelerated crop improvement. DH can be produced in planta by employing haploid inducer stock (HIS). Widely used HIS in maize is known to be governed by ZmPLA, ZmDMP, ZmPLD3, and ZmPOD65 genes. To develop such HIS in rice and wheat, we have identified putative orthologs of these genes using in silico approaches. The OsPLD1; TaPLD1, and OsPOD6; TaPOD8 were identified as putative orthologs of ZmPLD3 and ZmPOD65 in rice and wheat, respectively. Despite being closely related to ZmPLD3, OsPLD1 and TaPLD1 have shown higher anther-specific expression. Similarly, OsPOD6 and TaPOD8 were found closely related to the ZmPOD65 based on both phylogenetic and expression analysis. However, unlike ZmPLD3 and ZmPOD65, two ZmDMP orthologs have been found for each crop. OsDMP1 and OsDMP2 in rice and TaDMP3 and TaDMP13 in wheat have shown similarity to ZmDMP in terms of both sequence and expression pattern. Furthermore, analogs to maize DMP proteins, these genes possess four transmembrane helices making them best suited to be regarded as ZmDMP orthologs. Modifying these predicted orthologous genes by CRISPR/Cas9-based genome editing can produce a highly efficient HIS in both rice and wheat. Besides revealing the genetic mechanism of haploid induction, the development of HIS would advance the genetic improvement of these crops. [ABSTRACT FROM AUTHOR]

Key message: A BPH-resistant locus designated as Bph34 identified in Oryza nivara acc. IRGC104646 on long arm of chromosome 4 using high-resolution mapping with 50 K SNP chip. BPH resistance contributed by locus showed dominant inheritance in F2 and F3. The Bph34 locus is 91 kb in size and contains 11 candidate genes. In addition to SNP markers, SSR markers, RM16994 and RM17007 co-segregated with the BPH resistance. These two SSR markers can facilitate marker-assisted transfer of the Bph34 locus into elite rice cultivars in all labs.Abstract: Brown planthopper (BPH, Nilaparvata lugen Stål) is one of the most destructive insects of rice (Oryza sativa L.) causing significant yield losses annually. Exploiting host plant resistance to BPH and incorporating resistant genes in susceptible commercial cultivars is economical and environmentally friendly approach to manage this pest. Here, we report high-resolution mapping of a novel genetic locus for resistance to BPH, designated as Bph34 on long arm of rice chromosome 4. The locus was mapped using an interspecific F2 population derived from a cross between susceptible indica cultivar PR122 and BPH-resistant wild species, O. nivara acc. IRGC104646. Inheritance studies performed using F2 and F2:3 populations revealed the presence of single dominant gene. Construction of high-density linkage map using 50 K SNP chip (OsSNPnks) followed by QTL mapping identified single major locus at 28.8 LOD score between SNP markers, AX-95952039 and AX-95921548. The major locus contributing resistance to BPH designated as Bph34 and explained 68.3% of total phenotypic variance. The Bph34 locus is 91 Kb in size on Nipponbare reference genome-IRGSP-1.0 and contains 11 candidate genes. In addition to associated SNP markers, two SSR markers, RM16994 and RM17007, also co-segregated with the Bph34 which can be used efficiently for markers assisted transfer into elite rice cultivars across the labs. [ABSTRACT FROM AUTHOR]

The root-knot nematodes (RKN) (Meloidogyne graminicola) are a devastating threat to rice worldwide. The cultivated germplasm is either susceptible or moderately resistant to rice RKN. Therefore, there is a need to identify resistance sources against M. graminicola as an eco-friendly management strategy. The present study evaluated the host response of Oryza sativa genotypes comprising basmati, non-basmati improved varieties, their advanced breeding lines (83) and Oryza glaberrima accessions (42) against M. graminicola in the nematode-infested plot for two consecutive years. All O. sativa genotypes exhibited susceptible responses, while O. glaberrima accessions showed variable levels of resistance. Three of the O. glaberrima accessions (IRGC102196, IRGC102538 and IRGC102557) were highly resistant. M. graminicola significantly affected plant growth parameters in susceptible genotypes compared to resistant O. glaberrima accessions. The results were supported by histopathological studies that showed apparent giant cell formation in PR121 while penetration and development of M. graminicola juveniles were low in the O. glaberrima acc. IRGC102196. In silico analysis indicated that none of the reported nematode resistance genes from different crops had homology with the rice genome. The two anti-nematode genes (Oryzacystatin-I and Oryzacystatin-II) from O. sativa japonica revealed homology with O. sativa cv. PR121 and O. glaberrima acc. IRGC102206. Comparative analysis of these genes between PR121 and O. glaberrima acc. IRGC102206 resulted in the identification of SNPs/InDels that could be associated with nematode resistance. The identified SNPs/InDels could be validated, and further molecular studies are needed to provide insights into the resistance mechanism against rice RKN. [ABSTRACT FROM AUTHOR]

Background: Pigeonpea has remarkable contribution in flourishing the Indian agricultural economy but over the decades, its productivity has remained stagnant. Presence of genetic diversity in breeding population is the key to develop high yielding varieties. Therefore the current study was aimed to explore genetic divergence among pigeonpea genotypes. Methods: A set of 178 pigeonpea germplasm lines were evaluated in randomized block design to assess the genetic divergence and clustering pattern of pigeonpea genotypes. Observations on various yield component traits were recorded. For the estimation of the Fe and Zn content ICP-OES (Perkin Elmer USA) was used. Mahalanobis D² analysis was carried out to assess the genetic divergence. Result: Wide range of genetic diversity was revealed among lines for eleven traits studied. Mahalanobis D² analysis grouped all the genotypes into eleven non-overlapping clusters. The inter cluster D² values indicated that cluster IV and XI (21046.45) were the most diverse and cluster V and cluster VII (60.67) were the less diverse. Out of the eleven characters studied days to maturity, plant height and yield per plot contributed 93.32 per cent of the total divergence. Based on mean performances, cluster XI and cluster II were found to be beneficial for early flowering and early maturity genotypes, cluster V and cluster VII for number of pods per plant and yield per plot, respectively. The highest mean value for grain iron and zinc content was recorded in cluster III rendering simultaneous improvement for these traits. Therefore, trait-wise selection of diverse parents from different clusters would be desirable and beneficial. [ABSTRACT FROM AUTHOR]

Hot pepper (Capsicum annuum var. annuum) and bell pepper (C. annuum var. grossum) are the important crops of the Solanaceae family. In the present study, marker-assisted selection (MAS) was employed for interspecific leaf curl virus disease (LCVD) resistant gene introgression from hot pepper (S-343) to heat-tolerant bell pepper lines. Segregating populations were developed using resistant (S-343) and susceptible (bell pepper) genotypes for understanding the genetics of LCVD resistance. The micro-cage artificial screening technique was used for the phenotypic selection of LCVD resistant plants from progenies of each population. The F1 of all crosses were resistant to LCVD, while F2 and BC1F2 generations of all the crosses were segregated into 3:1 (resistant:susceptible) and BC1F1 generations of all crosses were a good fit to ratio 1:1 (resistant:susceptible) suggesting monogenic dominant control of LCVD resistance. In addition to phenotypic selection for LCVD resistance, MAS for non-pungency was done using 'BF7' and 'BR9'-SCAR primers along with the very stringent phenotyping (background selection) in backcrossed populations for most important fruit traits. The background selection was performed for the recovery of recurrent parent phenome and it was measured as shift in means of these important fruit traits. To the best of our knowledge, it is a novel experiment of introgression of LCVD resistance in heat tolerant bell pepper lines that led to the successful development of six improved LCVD resistant, heat-tolerant and non-pungent BC2F1 populations (LCVRS3SM-1, LCVRS3SM-2, LCVRS3SM-8, LCVRS3SM-4, LCVRS3SM-17, and LCVRS3SM-58) that will help in future bell pepper resistant breeding programs. [ABSTRACT FROM AUTHOR]

Begomoviruses, viz. squash leaf curl China virus and tomato leaf curl New Delhi virus causative diseases are major concerns of quantitative and qualitative losses in pumpkin (Cucurbita mose hata) worldwide. Punjab Agricultural University (PAU) in India has identified a resistant source PVR-1343) against mixed infection (MI-Sq/To) of these begomoviruses. Introgression of resistance in diverse genetic backgrounds requires the identification of quantitative trait loci (QTLs) associated with MI-Sq/To resistance. Phenotyping of 229 F21 progenies derived from the PVR-1343 P-135 cross revealed digenic recessive inheritance against MI - Sqfro resistance in PVR-1 343. To identify the genomic region, resistant and susceptible bulks were subjected to whole-genome resequencing along with their parents. The whole -genome resequence analysis of parents and bulks using QTLseq/QTLseqr approaches identified an overlapping 1.52 Mb region on chromosome 7 lqMI-Sqf[07. 1), while chromosomal region spanning 0. 87 Mb on chromosomel 7 0!MI-Sq/Toll. 1) was additionally identified by QTLseqr. However, the highest peak value on chromosome 7 with three algorithms {G', 8(SNP-index) and -logio (P value)} high-lighted the major contribution of qMI-Sqn-07. j in MI -Sq/To resistance. Nine polymorphic SNPs identified within the highly significant qM/- Sq/T07. 1 region were converted into KASP markers. KASP genotyping of Fi individuals narrowed down the qMI-scin'07. 1 interval to [03 kb region flanked by two markers, Cnio3914729 and Cm04018182. which contained 16 annotated genes and accounted for 59.84% of phenotypic variation. The Cmo4018182 KASPmarkeraccurately predicteddisease reaction in 91% of diverse Cucurbita genotypes and showed nonsynonym substitutions in the coding region of putative candidate SYNTAXIN- 121 gene. These findings pave the way for marker-assisted breeding and elucidating the underlying mechanism of begomovirus resistance in C. moschata. [ABSTRACT FROM AUTHOR]

Key message: Here, we report identification of a large effect QTL conferring Mungbean yellow mosaic India virus resistance introgressed from ricebean in blackgram variety Mash114. The tightly linked KASP markers would assist in marker-assisted-transfer of this region into Vigna species infected by MYMIV. Until recently, precise location of genes and marker-assisted selection was long thought in legumes such as blackgram due to lack of dense molecular maps. However, advances in next-generation sequencing based on high-throughput genotyping technologies such as QTL-seq have revolutionized trait mapping in marker-orphan crops. Using QTL-seq approach, we have identified a large-effect QTL for resistance to Mungbean yellow mosaic India virus (MYMIV) in blackgram variety Mash114. MYMIV is devastating disease responsible for huge yield losses in blackgram, greengram and other legumes. Mash114 showed consistent and high level of resistance to MYMIV since last nine years. Whole genome re-sequencing of MYMIV-resistant and susceptible bulks derived from RILs of cross KUG253 X Mash114 identified a large-effect QTL (qMYMIV6.1.1) spanning 3.4 Mb on chromosome 6 explaining 70% of total phenotypic variation. This region was further identified as an inter-specific introgression from ricebean. Linkage mapping using KASP markers developed from potent candidate genes involved in virus resistance identified the 500 kb genomic region equaling 1.9 cM on genetic map linked with MYMIV. The three KASP markers closely associated with MYMIV originated from serine threonine kinase, UBE2D2 and BAK1/BRI1-ASSOCIATED RECEPTOR KINASE genes. These KASPs can be used for marker-assisted transfer of introgressed segment into suitable backgrounds of Vigna species. [ABSTRACT FROM AUTHOR]

Utilization of “hidden genes” from wild species has emerged as a novel option for enrichment of genetic diversity for productivity traits. In rice we have generated more than 2000 lines having introgression from ‘A’ genome-donor wild species of rice in the genetic background of popular varieties PR114 and Pusa44 were developed. Out of these, based on agronomic acceptability, 318 lines were used for developing rice hybrids to assess the effect of introgressions in heterozygous state. These introgression lines and their recurrent parents, possessing fertility restoration ability for wild abortive (WA) cytoplasm, were crossed with cytoplasmic male sterile (CMS) line PMS17A to develop hybrids. Hybrids developed from recurrent parents were used as checks to compare the performance of 318 hybrids developed by hybridizing alien introgression lines with PMS17A. Seventeen hybrids expressed a significant increase in yield and its component traits over check hybrids. These 17 hybrids were re-evaluated in large-size replicated plots. Of these, four hybrids, viz., ILH299, ILH326, ILH867 and ILH901, having introgressions from O. rufipogon and two hybrids (ILH921 and ILH951) having introgressions from O. nivara showed significant heterosis over parental introgression line, recurrent parents and check hybrids for grain yield-related traits. Alien introgressions were detected in the lines taken as male parents for developing six superior hybrids, using a set of 100 polymorphic simple sequence repeat (SSR) markers. Percent introgression showed a range of 2.24 from in O. nivara to 7.66 from O. rufipogon. The introgressed regions and their putative association with yield components in hybrids is reported and discussed. [ABSTRACT FROM AUTHOR]

Being one of the most important staple dietary constituents globally, genetic enhancement of cultivated rice for yield, agronomically important traits is of substantial importance. Even though the climatic factors and crop management practices impact complex traits like yield immensely, the contribution of variation by underlying genetic factors surpasses them all. Previous studies have highlighted the importance of utilizing exotic germplasm, landraces in enhancing the diversity of gene pool, leading to better selections and thus superior cultivars. Thus, to fully exploit the potential of progenitor of Asian cultivated rice for productivity related traits, genome wide association study (GWAS) for seven agronomically important traits was conducted on a panel of 346 O. rufipogon accessions using a set of 15,083 high-quality single nucleotide polymorphic markers. The phenotypic data analysis indicated large continuous variation for all the traits under study, with a significant negative correlation observed between grain parameters and agronomic parameters like plant height, culm thickness. The presence of 74.28% admixtures in the panel as revealed by investigating population structure indicated the panel to be very poorly genetically differentiated, with rapid LD decay. The genome-wide association analyses revealed a total of 47 strong MTAs with 19 SNPs located in/close to previously reported QTL/genic regions providing a positive analytic proof for our studies. The allelic differences of significant MTAs were found to be statistically significant at 34 genomic regions. A total of 51 O. rufipogon accessions harboured combination of superior alleles and thus serve as potential candidates for accelerating rice breeding programs. The present study identified 27 novel SNPs to be significantly associated with different traits. Allelic differences between cultivated and wild rice at significant MTAs determined superior alleles to be absent at 12 positions implying substantial scope of improvement by their targeted introgression into cultivars. Introgression of novel significant genomic regions into breeder's pool would broaden the genetic base of cultivated rice, thus making the crop more resilient. [ABSTRACT FROM AUTHOR]

Cotton leaf curl disease (CLCuD), caused by a geminivirus complex, is the most serious disease of upland cotton in northwest India and Pakistan. It results in substantial losses in cotton yield and fibre quality. Due to continuous appearance of new viral strains, all the established CLCuD resistant stocks, extant and obsolete cultivars of upland cotton have become susceptible. Therefore, it became crucial to explore the novel sources of CLCuD resistance, as development of CLCuD resistant varieties is the most practical approach to manage this menace. Here, for the first time, we report introgression and mapping of CLCuD resistance from a ‘synthetic cotton polyploid’ to upland cotton. A backcross population (synthetic polyploid / Gossypium hirsutum Acc. PIL 43/G. hirsutum Acc. PIL 43) was developed for studying inheritance and mapping of CLCuD resistance. Dominance of CLCuD resistance was observed over its susceptibility. Two dominant genes were found to confer resistance to CLCuD. Molecular analysis through genotyping-by-sequencing revealed that chromosomes A01 and D07 harboured one CLCuD resistance gene each. [ABSTRACT FROM AUTHOR]

Being a model crop as well as a staple food crop, rice possesses a conspicuous position in plant sciences. Doubled haploid (DH) breeding in rice offers multiple advantages over conventional methods via accelerating the process of pure lines development. For ages, several methods have been devised for haploid production in rice. In vitro‐based methods have demonstrated their potential in DH production, but these methods are further impeded by stringent requirements and restricted to few species. Further, unlike maize, the in vivo DH breeding technology is still impractical in rice. Recent findings of the key molecular players behind the haploid induction (HI) trait in maize and rice have shown their potential in rice improvement programmes. In this review, we have discussed different strategies of HI in rice particularly focusing on recent progress made for developing haploid inducer stock (HIS) by employing both conventional and modern approaches. It also focuses on future implications of HIS so that it can be incorporated in the pipeline of modernized rice breeding. [ABSTRACT FROM AUTHOR]

Key message: A novel recessive bacterial blight resistance locus designated as a xa-45(t) was identified from Oryza glaberrima accession IRGC 102600B, transferred to O. sativa and mapped to the long arm of chromosome 8 using ddRAD sequencing approach. The identified QTL spans 80 kb region on Nipponbare reference genome IRGSP-1.0 and contains 9 candidate genes. An STS marker developed from the locus LOC_Os08g42410 was found co-segregating with the trait and will be useful for marker-assisted transfer of this recessive resistance gene in breeding programs. Bacterial blight, caused by Xanthomonas oryzae pv. oryzae, is one of the major constraints of rice productivity in Southeast Asia. In spite of having 44 bacterial blight resistance genes from cultivated rice and wild species, the durability of resistance is always at stake due to the continually evolving nature of the pathogen and lack of suitable chemical control. Here, we report high-resolution genetic mapping of a novel bacterial blight resistance gene tentatively designated as a xa-45(t) from an introgression line derived from Oryza glaberrima accession IRGC 102600B. This introgression line was crossed with the susceptible rice indica cultivar cv. Pusa 44 to generate F2 and F2:3 populations for inheritance and mapping studies. The inheritance studies revealed the presence of single recessive locus controlling resistance to the Xanthomonas pathotype seven. A high-density linkage map was constructed using double-digest restriction-associated DNA sequencing of 96 F2 populations along with the parents. The QTL mapping identified a major locus on the long arm of rice chromosome 8 with a LOD score of 33.22 between the SNP markers C8.26737175 and C8.26818765. The peak marker, C8.26810477, explains 49.8% of the total phenotypic variance and was positioned at 202.90 cM on the linkage map. This major locus spans 80 kb region on Nipponbare reference genome IRGSP-1.0 and contains 9 candidate genes. A co-segregating STS marker was developed from the LOC_Os08g42410 for efficient transfer of this novel gene to elite cultivars. [ABSTRACT FROM AUTHOR]

Breeding for terminal heat stress (THS) in Brassica juncea L. Czern & Coss is recognized as an imperative objective for sustained productivity in contemporary climatic changes. A fixed diversity stock of 491 genotypes was documented for wide range of variations for seed yield under natural terminal heat stress. A set of top 20 genotypes comprising introgression lines from wild species Erucastrum cardaminoides and B. tournefortii; derived B. juncea lines using B. carinata and B. napus; land races;, commercial cultivars and breeding lines, having the lowest heat susceptibility index and the least yield reduction under heat stress, have been identified as potential heat tolerant donors. A panel of 96 genotypes was constituted from this stock on the basis of their differential response to heat susceptibility index and seed yield reduction under natural THS. The constituted panel was evaluated for validation under controlled conditions for ten seed yield-related traits. Moderate to low correlations between SY and its related traits were observed in NS and THS conditions. Double digest restriction site associated DNA sequencing of 71 genotypes identified 18,258 SNPs after filtration. Least square means of all the traits under NS and THS conditions and the best linear unbiased predictors along with identified SNPs were used for genome-wide association study. A total of 34 SNPs under NS, 24SNPs under THS and 30SNPs using BLUP values were found to be associated with all seed yield-related traits. Chromosome B05 harbored the maximum number of SNPs (nine) followed by chromosomes A07 and A09 (eight SNPs each). SNPs under NS conditions could not be associated with THS. This is the first report on the identification of 24 marker-traits associations detected for SY and its component traits under THS conditions. It may be possible to develop the molecular markers for significant SNPs after due validation. The constituted panel may also serve as a source of allelic diversity for genes controlling various economic traits. The derived introgression lines as potential heat tolerant donors indicated the possibility of using wild species to breed for abiotic stress tolerance in Indian mustard. [ABSTRACT FROM AUTHOR]

• Begomoviruses infecting C. moschata were molecularly characterized as SLCCNV and ToLCNDV. • A novel resistant source (PVR-1343) against both the begomoviruses was identified. • Resistance against SLCCNV, ToLCNDV and their mixed infections was governed by digenic recessive inheritance. • The study revealed that resistance against these begomoviruses is mediated either by common or linked gene(s). Whitefly transmitted begomoviruses are the most destructive virus(es) that causes quantitative and qualitative losses to pumpkin (Cucurbita moschata) crop worldwide. In present study we have molecularly characterized three types of viral infections, which were caused by squash leaf curl China virus (SLCCNV), tomato leaf curl New Delhi virus (ToLCNDV), and their mixed infection (MI-Sq/To). Screening of diverse germplasm through whitefly (Bemisia tabaci mitotype Asia II) mediated artificial inoculation and PCR confirmed the 'PVR-1343' genotype as a resistance source against identified begomoviruses. To understand the genetic control of begomovirus resistant gene(s), segregating populations derived from crosses of 'PVR-1343' and four susceptible genotypes (MVSR-6711, Punjab Samrat, MBN-6242 and P-278) inoculated with SLCCNV, ToLCNDV and MI-Sq/To by whitefly in closed environment for three consecutive years (2018–2020). Disease scoring at 75 days after sowing rendered all F 1 progenies as susceptible indicating recessive nature of resistance with no maternal or cytoplasmic effects. Chi-square analysis indicated a good fit of 9(S):3(MS):3(MR):1(R) ratio in F 2 progenies of all crosses. Backcross of the F 1 's to the resistant parent segregated into 1:1:1:1 ratio, while all progeny were susceptible in backcross of the F 1 's with susceptible parent. Phenotypic segregation ratio of F 2:3 confirmed the F 2 genotypic ratio of 1:2:2:4:1:2:1:2:1. This substantiated that multiple begomovirus resistance in 'PVR-1343' is controlled by digenic recessive genes. Moreover, F 2:3 progenies resistant to SLCCNV were also resistant to ToLCNDV and MI-Sq/To and vice versa, suggesting that common or tightly linked gene(s) might be involved in resistance to both viruses. [ABSTRACT FROM AUTHOR]

Increasing the rice productivity from the current 10 to 12 tons/ha to meet the demand of estimated 8.8 billion people in 2035 is posing a major challenge. Wild relatives of rice contain some novel genes which can help in improving rice yield. Spikelet per panicle (SPP) is a valuable trait for determining yield potential in rice. In this study, a major QTL for increasing SPP has been identified, mapped, and transferred from African wild rice O. longistaminata to O. sativa (L.). The QTL was mapped on the long arm of chromosome 2 in a 167.1 kb region flanked by SSR markers RM13743 and RM13750, which are 1.0 cM apart, and is designated as qSPP2.2. The QTL explained up to 30% of phenotypic variance in different generations/seasons and showed positive additive effect of allele contributed by O. longistaminata. In addition, O. longistaminata allele in qSPP2.2 contributed to increase in grains per panicle, but decrease in the tillers per plant. The 167.1 kb region contains 23 predicted genes. Based on the functional annotation, three genes, LOC_Os02g44860, LOC_Os02g44990, and LOC_Os02g45010, were selected as putative candidates for characterization. Sequence analysis of the three genes revealed functional variations between the parental lines for LOC_Os02g44990 and a variation in 5′UTR for LOC_Os02g45010 which will help further to identify putative candidate gene(s). This is the first yield component QTL to be identified, mapped, and transferred from O. longistaminata. [ABSTRACT FROM AUTHOR]

Breeding for terminal heat stress (THS) in Brassica juncea L. Czern & Coss is recognized as an imperative objective for sustained productivity in contemporary climatic changes. A fixed diversity stock of 491 genotypes was documented for wide range of variations for seed yield under natural terminal heat stress. A set of top 20 genotypes comprising introgression lines from wild species Erucastrum cardaminoides and B. tournefortii; derived B. juncea lines using B. carinata and B. napus; land races;, commercial cultivars and breeding lines, having the lowest heat susceptibility index and the least yield reduction under heat stress, have been identified as potential heat tolerant donors. A panel of 96 genotypes was constituted from this stock on the basis of their differential response to heat susceptibility index and seed yield reduction under natural THS. The constituted panel was evaluated for validation under controlled conditions for ten seed yield-related traits. Moderate to low correlations between SY and its related traits were observed in NS and THS conditions. Double digest restriction site associated DNA sequencing of 71 genotypes identified 18,258 SNPs after filtration. Least square means of all the traits under NS and THS conditions and the best linear unbiased predictors along with identified SNPs were used for genome-wide association study. A total of 34 SNPs under NS, 24SNPs under THS and 30SNPs using BLUP values were found to be associated with all seed yield-related traits. Chromosome B05 harbored the maximum number of SNPs (nine) followed by chromosomes A07 and A09 (eight SNPs each). SNPs under NS conditions could not be associated with THS. This is the first report on the identification of 24 marker-traits associations detected for SY and its component traits under THS conditions. It may be possible to develop the molecular markers for significant SNPs after due validation. The constituted panel may also serve as a source of allelic diversity for genes controlling various economic traits. The derived introgression lines as potential heat tolerant donors indicated the possibility of using wild species to breed for abiotic stress tolerance in Indian mustard. [ABSTRACT FROM AUTHOR]