Deepa Jaganathan

Fast-track introgression of “QTL-hotspot” for root traits and other drought tolerance traits in JG 11, an elite and leading variety of chickpea

A “QTL‐hotspot” containing quantitative trait loci (QTL) for several root and drought tolerance traits was transferred through marker‐assisted backcrossing into JG 11, a leading variety of chickpea (Cicer arietinum L.) in India from the donor parent ICC 4958. Foreground selection with up to three simple sequence repeat markers, namely TAA170, ICCM0249, and STMS11, and background selection with up to 10 amplified fragment length polymorphism primer combinations was undertaken. After undertaking three backcrosses with foreground and background selection and selfing, 29 BC3F2 plants homozygous for two markers (ICCM0249 and TAA170) were selected and referred as introgression lines (ILs). Root trait phenotyping of these ILs showed higher rooting depth (RDp) (average 115.21 ± 2.24 cm) in all 29 ILs, better root length density (RLD) (average 0.41 ± 0.02 cm cm−3) in 26 ILs, and higher root dry weight (RDW) (average 1.25 ± 0.08 g per cylinder) as compared to the recurrent parent, JG 11 (111.70 cm for RDp, 0.39 cm cm−3 for RLD, and 1.10 g per cylinder for RDW), as well as the donor parent, ICC 4958 (114.20 cm for RDp, 0.45 cm cm−3 for RLD, and 1.25 g per cylinder for RDW). These ILs, developed in 3 yr, after multilocation field trials may be released as improved variety with enhanced drought tolerance.

Prioritization of candidate genes in “ QTL-hotspot ” region for drought tolerance in chickpea ( Cicer arietinum L.)

A combination of two approaches, namely QTL analysis and gene enrichment analysis were used to identify candidate genes in the “QTL-hotspot” region for drought tolerance present on the Ca4 pseudomolecule in chickpea. In the first approach, a high-density bin map was developed using 53,223 single nucleotide polymorphisms (SNPs) identified in the recombinant inbred line (RIL) population of ICC 4958 (drought tolerant) and ICC 1882 (drought sensitive) cross. QTL analysis using recombination bins as markers along with the phenotyping data for 17 drought tolerance related traits obtained over 1–5 seasons and 1–5 locations split the “QTL-hotspot” region into two subregions namely “QTL-hotspot_a” (15 genes) and “QTL-hotspot_b” (11 genes). In the second approach, gene enrichment analysis using significant marker trait associations based on SNPs from the Ca4 pseudomolecule with the above mentioned phenotyping data, and the candidate genes from the refined “QTL-hotspot” region showed enrichment for 23 genes. Twelve genes were found common in both approaches. Functional validation using quantitative real-time PCR (qRT-PCR) indicated four promising candidate genes having functional implications on the effect of “QTL-hotspot” for drought tolerance in chickpea.

QTL-seq for rapid identification of candidate genes for 100-seed weight and root/total plant dry weight ratio under rainfed conditions in chickpea

Summary Terminal drought is a major constraint to chickpea productivity. Two component traits responsible for reduction in yield under drought stress include reduction in seeds size and root length/root density. QTL‐seq approach, therefore, was used to identify candidate genomic regions for 100‐seed weight (100SDW) and total dry root weight to total plant dry weight ratio (RTR) under rainfed conditions. Genomewide SNP profiling of extreme phenotypic bulks from the ICC 4958 × ICC 1882 population identified two significant genomic regions, one on CaLG01 (1.08 Mb) and another on CaLG04 (2.7 Mb) linkage groups for 100SDW. Similarly, one significant genomic region on CaLG04 (1.10 Mb) was identified for RTR. Comprehensive analysis revealed four and five putative candidate genes associated with 100SDW and RTR, respectively. Subsequently, two genes (Ca_04364 and Ca_04607) for 100SDW and one gene (Ca_04586) for RTR were validated using CAPS/dCAPS markers. Identified candidate genomic regions and genes may be useful for molecular breeding for chickpea improvement.

Chickpea Individual and consensus genetic maps for ICC 283 x ICC 826, ICC 4958 x ICC 1882

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. CMap Visualization Links: ICC 283 x ICC 8261 ICC 4958 x ICC 1882 Consensus map

Intra-specific genetic map of ICC 4958 x ICC 1882 by Genotyping-By-Sequencing approach

To enhance the marker density in the “QTL-hotspot” region, harboring several QTLs for drought tolerance-related traits identified on linkage group 04 (CaLG04) in chickpea recombinant inbred line (RIL) mapping population ICC 4958 × ICC 1882, a genotyping-by-sequencing approach was adopted. In total, 6.24 Gb data from ICC 4958, 5.65 Gb data from ICC 1882 and 59.03 Gb data from RILs were generated, which identified 828 novel single-nucleotide polymorphisms (SNPs) for genetic mapping. Together with these new markers, a high-density intra-specific genetic map was developed that comprised 1,007 marker loci spanning a distance of 727.29 cM. QTL analysis using the extended genetic map along with precise phenotyping data for 20 traits collected over one to seven seasons identified 49 SNP markers in the “QTL-hotspot” region. These efforts have refined the “QTL-hotspot” region to 14 cM. In total, 164 main-effect QTLs including 24 novel QTLs were identified. CMap Visualization Links: GBS-SNP Map_ICC 4958 x ICC 1882