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 BC ₃ F ₃ in Pusa 372; 20 BC ₂ F ₃ in Pusa 362, and 21 BC ₃ F ₃ 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.

Globally, chickpea production is severely affected by salinity stress. Understanding the genetic basis for salinity tolerance is important to develop salinity tolerant chickpeas. A recombinant inbred line (RIL) population developed using parental lines ICCV 10 (salt-tolerant) and DCP 92-3 (salt-sensitive) was screened under field conditions to collect information on agronomy, yield components, and stress tolerance indices. Genotyping data generated using Axiom^®CicerSNP array was used to construct a linkage map comprising 1856 SNP markers spanning a distance of 1106.3 cM across eight chickpea chromosomes. Extensive analysis of the phenotyping and genotyping data identified 28 quantitative trait loci (QTLs) explaining up to 28.40% of the phenotypic variance in the population. We identified QTL clusters on CaLG03 and CaLG06, each harboring major QTLs for yield and yield component traits under salinity stress. The main-effect QTLs identified in these two clusters were associated with key genes such as calcium-dependent protein kinases, histidine kinases, cation proton antiporter, and WRKY and MYB transcription factors, which are known to impart salinity stress tolerance in crop plants. Molecular markers/genes associated with these major QTLs, after validation, will be useful to undertake marker-assisted breeding for developing better varieties with salinity tolerance.

Unravelling the genetic architecture underlying yield components and agronomic traits is important for enhancing crop productivity. Here, a recombinant inbred line (RIL) population, developed from ICC 4958 and DCP 92–3 cross, was used for constructing linkage map and QTL mapping analysis. The RIL population was genotyped using a high-throughput Axiom^®CicerSNParray, which enabled the development of a high-density genetic map consisting of 3,818 SNP markers and spanning a distance of 1064.14 cM. Analysis of phenotyping data for yield, yield components and agronomic traits measured across three years together with genetic mapping data led to the identification of 10 major-effect QTLs and six minor-effect QTLs explaining up to 59.70% phenotypic variance. The major-effect QTLs identified for 100-seed weight, and plant height possessed key genes, such as C3HC4 RING finger protein, pentatricopeptide repeat (PPR) protein, sugar transporter, leucine zipper protein and NADH dehydrogenase, amongst others. The gene ontology studies highlighted the role of these genes in regulating seed weight and plant height in crop plants. The identified genomic regions for yield, yield components, and agronomic traits, and the closely linked markers will help advance genetics research and breeding programs in chickpea.

Grass pea (Lathyrus sativus L.) is an important food crop cultivated in dryland agricultural ecosystem. It is an important source of dietary protein to millions of people living in low-income countries in South-east Asia and Africa. The present study emphasises the development of genomic resources and their application in marker–trait association for plant phenology and yield-related traits in lathyrus. In silico mining of nucleotide sequences identified 203 simple sequence repeat (SSR) motifs, of which trimer repeats (62%) were most abundant followed by tetramer (19%), hexamer (10%), pentamer (6%) and dimer (3%) nucleotide repeats. Of 150 SSR markers screened, 60 markers were amplified 75 alleles from 50 germplasm lines with 2–3 alleles per locus and the polymorphic information content of 0.45 was observed. We report 6 significant marker–trait associations using the developed SSR markers for plant phenology and yield-related traits following mixed linear model (Q+K) analysis. Gene ontology search of trait linked markers revealed marker regions encoding genes related to homeobox-leucine zipper protein ATHB-6-like, rubredoxin family protein, and cationic peroxidise. Understanding the association of novel alleles in trait expression will play a significant role in future lathyrus crop improvement programmes.