Chickpea is one of the most important grain legume crops of India. Chickpea production is constantly under threat from various biotic and abiotic stresses. Dry root rot (DRR) caused by the necrotic fungus Macrophomina phaseolina is an important threat to chickpea productivity. Identifying resistant sources is the first step in breeding resilient varieties. In the present study, 56 genotypes from different chickpea regions of India were evaluated for their response to DRR using different screening methods, including paper towel, pot inoculation, and mycelium suspension drenching, followed by screening promising lines in the sick plot. This multi-method approach is crucial as genotypes' responses to disease can vary depending on the screening technique used. Among the tested genotypes, RVSSG 64, demonstrated consistent resistance across all screening methods. Additionally, genotypes RVSSG 58, JSC 37, H14-04, and H14-21 with varying degrees of resistance were also identified.

Yield is an important and complex quantitative trait that is profoundly affected by environmental factors. Currently, dry root rot disease causes more yield reduction in chickpea. Exploiting an association between yield and its associated traits is required to increase the selection efficiency. Therefore, this study approaches correlation analysis, principal components and path coefficient analysis to evaluate variation in F2 segregating populations. The present investigation was conducted at the Department of Agricultural Botany Farm, Post Graduate Institute, Mahatma Phule Krishi Vidyapeeth, Rahuri, Maharashtra, from October 2017 to November 2022. The resistant (JSC-37) and susceptible (Vijay and Digvijay) parents to dry root rot were used to develop F2 mapping population, which comprised 150 and 38 individuals and later F3 population was screened for dry root rot disease. Correlation analysis revealed significant positive correlation of all characters with seed yield per plant in F2 population of both crosses except days to flowering. Negative association of disease incidence with seed yield was shown in both crosses. Path coefficient study revealed a high direct effect of the number of pods per plant on seed yield per plant in both crosses. Particularly, the number of secondary branches per plant, the number of pods per plant and biological yield were simultaneously shown to be the primary cause of variations in Principal Component Analysis (PCA) analysis in both crosses. As a result, these traits could be regarded as the most suitable choice factors in breeding programs for developing high yielding varieties.

Chickpeas are a rich source of protein and essential nutrients, making them a staple in many diets worldwide. They are also drought-tolerant, which makes them a valuable crop for improving food security in arid regions. Thirty chickpea genotypes were evaluated under irrigated and rainfed condition separately Randomized Complete Block Design (RCBD) with three replications at Post Graduate Institute Farm, MPKV Rahuri to study yield, physiological and biochemical response for drought tolerance in Rabi 2022-2023. Analysis of variance observed significant difference among studied genotypes in irrigated and rainfed condition for all the characters studied. Genetic variation exists in diverse chickpea genotypes for bio-physiological, morphological and yield attributing characters which can be explored for genetic improvement. As expected, water stress adversely affected the physiological, biochemical and yield responses of all the chickpea genotypes evaluated. The performance of genotypes Phule G-16318 and Phule G-1420-13-6 was observed to be stable for most of the characters such as Chlorophyll index, membrane stability index, relative water content, photosynthesis rate, proline content under moisture stress condition. Similarly, both the genotypes with minimal reductions in seed yield, 100 seed weight, pod number and biomass plant-1 under rainfed condition, can serve as donors for drought tolerance in chickpea improvement programs.

Rice is one of the important food crops of the world. Fragrance is one of the important properties of rice which determines the market price. In the present study, 53 rice genotypes comprising landraces, advanced lines and improved varieties were characterized for their aroma based on sensory testing by KOH method, while molecular characterization of 48 lines was conducted using functional (gene specific) and simple sequence repeat (SSR) markers. The molecular analysis for 48 genotypes by SSR markers along with functional markers (Badex7-5, FMbadh2-E7) showed distinctive differentiation between the genotypes as aromatic or non-aromatic. The SSR markers also confirmed the existence of other QTL on chromosome 3 and 4 (aro3-1, aro4-1). The data obtained from the molecular studies was used to determine the genetic relationship and to construct the dendrogram. The genotypes were grouped into 3 clusters and 8 sub-clusters based on the presence of aroma. The molecular studies confirmed the sensory studies and dendrogram analysis grouped all these genotypes according to their similarities and relationships

Background: Pigeonpea is an important protein-rich legume and one of the potential crops for rainfed agriculture in many parts of the semi-arid tropics. Worldwide, India ranks first both in area and production. Despite that, the productivity levels in India are low because of various biotic and abiotic stresses, out of which Sterility mosaic disease (SMD), which is caused by Pigeonpea Sterility Mosaic Virus (PPSMV), is a severe constraint during crop production. In the context of the above facts, resistant breeding is one of the most economical and eco-friendly approaches. The present investigation aimed to identify microsatellite markers linked to SMD resistance and potential resistant genetic resources. In this field- laboratory investigation carried out during 2017-2018, thirty genotypes and susceptible check ICP 8863 were evaluated in a randomized block design (RBD) with two replications in SMD sick plots. Observations were recorded based on visual symptoms for SMD incidence, and percent disease incidence (PDI) was calculated. In addition, a molecular study for the same genotypes was carried out with a total of 20 SSR markers. Out of 20 SSR primers, only 16 were amplified, from which only a single SSR marker (AHSSR20) showed polymorphism while the remaining 15 were monomorphic. The marker AHSSR20 have the potential to discriminate resistant and susceptible genotypes. AHSSR 20 primer assign 160 bp bands in resistant genotypes viz., BDN-711, PT-04-281, and PT-704-1-2 while ever, 172 bp bands assign in susceptible genotypes viz. ICP-8863, PT-04-378, PT-012-20, and PT-016-3. Accordingly, we conclude that AHSSR20 is a potent marker that can be helpful to discriminate between susceptible and resistant genotypes and can be used for direct selection of resistant genotypes during early segregating generation and marker-assisted breeding.

Genetic diversity was assessed for 2 popular varieties and 5 promising lines of rabi sorghum by using11 SSR markers. The marker Xiabt312 reported 100% polymorphism rate followed by Xtxp15 (85.70%) and mSbCIR300 (85.71%). The sorghum varieties studied for this analysis showed the polymorphism information content (PIC) ranged from 0.25 to 0.87 with a mean of 0.67 indicates higher diversity within them. Clustering analysis based on the genetic dissimilarity grouped the 7 lines into 2 major and 4 sub clusters and grouping was in good agreement with pedigree. Cluster II was the largest cluster with 4 genotypes followed by cluster I with 3 genotypes. The rabi sorghum genotypes viz., M35-1, RSV-1876 and RSLG-2422 were placed in cluster I and Phule Anuradha, RSV-2371, RSV-1910 and RSV-1988 placed in cluster II. Clustering based on SSR molecular profile of the genotypes shows that there is a distinct variability among the genotypes under this study. The selected markers have great potential in DNA fingerprinting in sorghum which in future could be integrated with DUS data descriptors for effective cultivar identification and differentiation.

Wheat is one of the major staple cereal food crops in India. However, most of the wheat-growing areas experience several biotic and abiotic stresses, resulting in poor quality grains and reduced yield. To ensure food security for the growing population in India, there is a compelling need to explore the untapped genetic diversity available in gene banks for the development of stress-resistant/tolerant cultivars. The improvement of any crop lies in exploring and harnessing the genetic diversity available in its genetic resources in the form of cultivated varieties, landraces, wild relatives, and related genera. A huge collection of wheat genetic resources is conserved in various gene banks across the globe. Molecular and phenotypic characterization followed by documentation of conserved genetic resources is a prerequisite for germplasm utilization in crop improvement. The National Genebank of India has an extensive and diverse collection of wheat germplasm, comprising Indian wheat landraces, primitive cultivars, breeding lines, and collection from other countries. The conserved germplasm can contribute immensely to the development of wheat cultivars with high levels of biotic and abiotic stress tolerance. Breeding wheat varieties that can give high yields under different stress environments has not made much headway due to high genotypes and environmental interaction, non-availability of truly resistant/tolerant germplasm, and non-availability of reliable markers linked with the QTL having a significant impact on resistance/tolerance. The development of new breeding technologies like genomic selection (GS), which takes into account the G × E interaction, will facilitate crop improvement through enhanced climate resilience, by combining biotic and abiotic stress resistance/tolerance and maximizing yield potential. In this review article, we have summarized different constraints being faced by Indian wheat-breeding programs, challenges in addressing biotic and abiotic stresses, and improving quality and nutrition. Efforts have been made to highlight the wealth of Indian wheat genetic resources available in our National Genebank and their evaluation for the identification of trait-specific germplasm. Promising genotypes to develop varieties of important targeted traits and the development of different genomics resources have also been highlighted.

Spine gourd (Momordica dioica Roxb.) is a highly nutritious vegetable crop with dioecious reproductive nature. Forty-eight spine gourd genotypes including 32 female and 16 male genotypes were assessed for molecular divergence to establish phenotypic relationships using ISSR markers. Twenty-two out of a total of 25 ISSR primers studied yielded a total of 88 bands of which 80 bands were polymorphic, with three of them being unique in their profile. Each primer thus produced a mean of 4.0 bands per marker, with 3.64 mean polymorphic bands per marker. Fifteen primers showed 100 percent polymorphism. In the dendrogram, genotypes were distinguished from each other with a similarity range of 0.465 to 0.959. A wider range of molecular diversity detected by ISSR markers reflected the presence of a high level of genetic variation forming different 5 broad groups of clusters. The clustering pattern based on molecular variation during this investigation revealed five clusters; of which cluster three had twenty-eight (all 16 malealong with 12 female genotypes) genotypes; while cluster 4 and 5 were mono-genotypic.

Association mapping (AM), also known as genome-wide association studies (GWAS), is increasingly being employed in crop plants for the identification of QTL/genes and marker-trait associations (MTAs) in natural populations. Large numbers of such associations have been identified for variety of traits in different crop plants. However, not many of these associations have been used practically in the crop improvement program due to lack of validation. Although there are different ways through which the results of AM/GWAS could be validated, the best approach is to develop a biparental population for the trait of interest. An overview of the steps involved in the validation of results of AM using biparental mapping population in plants is provided in this chapter.

We had the fortune of starting our scientific/research careers in the Molecular Biology and Crop Biotechnology Laboratory of Professor P.K. Gupta at Ch. Charan Singh University, Meerut, UP, India. Here, we describe the most important scientific contributions of our beloved mentor in the area of cytotaxonomy, cytogenetics, mutation breeding, quantitative genetics, molecular biology, crop biotechnology and plant genomics, on his 85th birthday. Important contributions made in the development and use of genomics resources including the development and use of different kinds of molecular markers, genetic and physical mapping, quantitative trait locus (QTL) interval mapping, genome-wide association mapping and molecular breeding including marker-assisted selection have been briefly summarized. Efforts have been also made to give readers a glimpse of important contributions in the study of cytology/apomixis of grasses, cytotaxonomic studies in asteraceae/fabaceae, nuclear/repetitive DNA content in Lolium, interspecific/intergeneric relationships involving the genus Hordeum and re-examining taxonomy of the tribe Triticeae.

Chickpea is an important cool season legume crop. The breeding efforts in chickpea are often hampered due to the narrow genetic base. Availability of diverse germplasm is an essential requirement for any crop improvement programme. This can facilitate development of desirable gene combinations and subsequently the improved cultivars. In any marker-assisted selection (MAS) programme, study of parental polymorphism using QTL linked markers is a pre-requisite for screening of desired genotypes. Any such study involving use of markers chosen randomly can only tell the diversity of the parents, but does not guarantee success of the MAS. The present study was undertaken to study the suitability of the SSR markers from the QTL-hotspot region linked with drought tolerance related traits in different genetic background. The study of polymorphism of the QTL-hotspot linked SSR markers NCPGR127, NCPGR21, TAA170, ICCM0249, STMS11, TR11 and GA24 between drought tolerant genotype ICC-4958 and remaining 32 chickpea genotypes revealed that most of the genotypes had monomorphic alleles as that of ICC-4958, while only a few genotypes showed polymorphic alleles. The markers that are found polymorphic between ICC-4958 and other chickpea genotypes can be used directly for foreground selection in MAS as they are mapped in the QTL-hotspot region. However, in cases where these are monomorphic, additional markers from QTL-hotspot region need to be screened. Besides validating the suitability of these markers, we also validated SSR markers that can be used for the background selection. Of the 21 SSR markers, 15 were found polymorphic between ICC-4958 and other genotypes suggesting their usefulness in the background selection.

Quantitative trait loci mapping has become a common practice in crop plants and can be accomplished using either biparental populations following interval mapping or natural populations following the approach of association mapping. Because of its ability to use the natural diversity and to search for functional variants in a broader germplasm, association mapping is becoming popular among researchers. An overview of the different steps involved in association mapping in plants is provided in this chapter.

The continuous increase in global population prompts increased wheat production. Future wheat (Triticum aestivum L.) breeding will heavily rely on dissecting molecular and genetic bases of wheat yield and related traits which is possible through the discovery of quantitative trait loci (QTLs) in constructed populations, such as recombinant inbred lines (RILs). Here, we present an evaluation of 92 RILs in a bi-parental RIL mapping population (the International Triticeae Mapping Initiative Mapping Population [ITMI/MP]) using newly generated phenotypic data in 3-year experiments (2015), older phenotypic data (1997-2009), and newly created single nucleotide polymorphism (SNP) marker data based on 92 of the original RILs to search for novel and stable QTLs. Our analyses of more than 15 unique traits observed in multiple experiments included analyses of 46 traits in three environments in the USA, 69 traits in eight environments in Germany, 149 traits in 10 environments in Russia, and 28 traits in four environments in India (292 traits in 25 environments) with 7584 SNPs (292 x 7584 = 2 214 528 data points). A total of 874 QTLs were detected with limit of detection (LOD) scores of 2.01-3.0 and 432 QTLs were detected with LOD > 3.0. Moreover, 769 QTLs could be assigned to 183 clusters based on the common markers and relative proximity of related QTLs, indicating gene-rich regions throughout the A, B, and D genomes of common wheat. This upgraded genotype-phenotype information of ITMI/MP can assist breeders and geneticists who can make crosses with suitable RILs to improve or investigate traits of interest.

The Translational Chickpea Genomics Consortium (TCGC) was set up to increase the production and productivity of chickpea (Cicer arietinum L.). It represents research institutes from six major chickpea growing states (Madhya Pradesh, Maharashtra, Andhra Pradesh, Telangana, Karnataka and Uttar Pradesh) of India. The TCGC team has been engaged in deploying modern genomics approaches in breeding and popularizing improved varieties in farmers’ fields across the states. Using marker-assisted backcrossing, introgression lines with enhanced drought tolerance and fusarium wilt resistance have been developed in the genetic background of 10 elite varieties of chickpea. Multi-location evaluation of 100 improved lines (70 desi and 30 kabuli) during 2016–2017 and 2018–2019 enabled the identification of top performing desi and kabuli lines. In total, 909 Farmer Participatory Varietal Selection trials were conducted in 158 villages in 16 districts of the five states, during 2017–2018, 2018–2019, and 2019–2020, involving 16 improved varieties. New molecular breeding lines developed in different genetic backgrounds are potential candidates for national trials under the ICAR-All India Coordinated Research Project on Chickpea. The comprehensive efforts of TCGC resulted in the development and adoption of high-yielding varieties that will increase chickpea productivity and the profitability of chickpea growing farmers.

In the present investigation, seven chickpea genotypes and their twenty one crosses (excluding reciprocals) were grown at Post Graduate Institute Farm, Mahatma Phule Krishi Vidyapeeth, Rahuri, in Randomized Block Design (RBD) with three replications. Combining ability analysis was carried out in 7 x 7 parental half diallel fashion for grain yield and its components in chickpea. General combining ability and specific combining ability variances were highly significant for all the characters indicating importance of both additive as well as non-additive type of gene actions in the inheritance of studied traits i.e., days to 50% flowering, days to maturity, plant height, plant spread, number of primary branches per plant, number of secondary branches per plant, number of fruiting branches per plant, number of pods per plant, number of seeds per plant, 100 seed weight and seed yield per plant. The parent Phule Vikram, JAKI-9218, Digvijay and GNG-2207 were high yielding with good general combining ability for grain yield per plant and some of its components, which can be used in future hybridization programme. Whereas, the crosses GNG-2207 X Digvijay, Digvijay x WR-315 and Phule Vikram x Digvijay recorded the highest sca effects. These crosses should be exploited for obtaining recombinants in advance segregating generations.

Genetic diversity study was conducted in 49 chickpea (Cicer arietinum L.) genotypes using Mahalanobis D2 Statistics. Based on D2 values, 49 genotypes were grouped into 17 clusters. The cluster III consisted of maximum 13 genotypes followed by Cluster I and cluster II which both had 10 genotypes. Inter cluster values varied from 4.31 to 26.36. The maximum inter cluster distance was recorded between cluster IX and XIII (26.36). Characters 100 seed weight (62.07%), days to 50% flowering (17.94%) and canopy temperature depression (5.27%) contributed maximum towards diversity. On the basis of cluster mean values, cluster XIII was superior for yield per plot and 100 seed weight. The genotypes belonging to the clusters separated by high genetic distance could be used in hybridization programme for obtaining a wide spectrum of variation among the segregants.

Chickpea is an important cool-season food legume grown and consumed throughout the world. Amongst various biotic stresses which affect chickpea production, wilt caused by Fusarium oxysporum is one of the important diseases. Over the years, different races of this pathogen have been identified and characterized. Because of the significance of this disease, it is a prerequisite that the chickpea genotypes (both new as well as old) must be evaluated for their reaction against wilt before they are released as a new variety. In the present study, 31 chickpea genotypes comprising promising lines and earlier released varieties were evaluated for wilt resistance in the wilt sick plot. In addition, 18 SSR markers, which were earlier reported to be linked with wilt resistance QTLs were used to characterize these genotypes. The wilt reaction ranged from resistant [0% (WR 315) to 10% (PG 15,016, Vijay)] to highly susceptible type [53.33% (BG 3065; NDG 14–11) to 100% (JG 62)]. It was observed that majority of the lines from North India were susceptible to wilt, while those from the state of Maharashtra (western India) were resistant indicating that the genotypes from different parts of India have resistance against different races which are prevalent in different regions. It was also observed that molecular markers could group these chickpea genotypes largely based on their reaction against wilt and to some extent on the basis of their pedigree.