Novel Salinity Tolerance Loci in Chickpea Identified in Glasshouse and Field Environments

Abstract

A better understanding of the genetics of salinity tolerance in chickpea would enable breeding of salt tolerant varieties, offering potential to expand chickpea production to marginal, salinity-affected areas. A Recombinant Inbred Line population was developed using accelerated-Single Seed Descent of progeny from a cross between two chickpea varieties, Rupali (salt-sensitive) and Genesis836 (salt-tolerant). The population was screened for salinity tolerance using high-throughput image-based phenotyping in the glasshouse, in hydroponics, and across 2 years of field trials at Merredin, Western Australia. A genetic map was constructed from 628 unique in-silico DArT and SNP markers, spanning 963.5 cM. Markers linked to two flowering loci identified on linkage groups CaLG03 and CaLG05 were used as cofactors during genetic analysis to remove the confounding effects of flowering on salinity response. Forty-two QTL were linked to growth rate, yield, and yield component traits under both control and saline conditions, and leaf tissue ion accumulation under salt stress. Residuals from regressions fitting best linear unbiased predictions from saline conditions onto best linear unbiased predictions from control conditions provided a measure of salinity tolerance per se, independent of yield potential. Six QTL on CaLG04, CaLG05, and CaLG06 were associated with tolerance per se. In total, 21 QTL mapped to two distinct regions on CaLG04. The first distinct region controlled the number of filled pods, leaf necrosis, seed number, and seed yield specifically under salinity, and co-located with four QTL linked to salt tolerance per se. The second distinct region controlled 100-seed weight and growth-related traits, independent of salinity treatment. Positional cloning of the salinity tolerance-specific loci on CaLG04, CaLG05, and CaLG06 will improve our understanding of the key determinants of salinity tolerance in chickpea.

The genetics of vigour-related traits in chickpea (Cicer arietinum L.): insights from genomic data

“…The development of crop plant ideotypes with improved vigour is a strategy that will not only promote strong early establishment to help overcome weed competition but also improve the subsequent performance and growth of plants under unfavourable conditions, i.e. low temperature (Fonteyne et al 2015), salinity (McHughen 1987;Yeo et al 1990;Platten et al 2013;Atieno et al 2021) and drought (Sivasakthi et al 2018). Several studies in other crops have reported an association between vigour and disease resistance, where QTL for vigour overlapped with field resistance to late blight in potato (Collins et al 1999), phytophthora root rot in red raspberry (Graham et al 2011) and fusarium basal rot in onion (Taylor et al 2019a, b).…”

“…Similarly, Sabaghpour and Rao (2003) used a chickpea RIL population and found positive correlations between 100-seed weight (100SDW) and initial growth vigour (20 days after germination), as well as leaf size, leaf weight and plant height. In chickpea, seed size and vigour-related traits may be linked genetically since QTL for both traits have been mapped to the same region on Ca4 (Varshney et al 2014;Kale et al 2015;Sivasakthi et al 2018;Atieno et al 2021;Barmukh et al 2021). Additionally, a myo-inositol monophosphatase (CaIMP) gene, located within 2 Mb of a 100SDW QTL on Ca1 (Varshney et al 2014;Jaganathan et al 2015), was reported to not only contribute to chickpea seed size but also improve seed germination and seedling growth under abiotic stress conditions (Saxena et al 2013;Joshi-Saha and Reddy 2015;Dwivedi et al 2017).…”

Evidence for the Application of Emerging Technologies to Accelerate Crop Improvement – A Collaborative Pipeline to Introgress Herbicide Tolerance Into Chickpea

“…Cycle time, or generation interval, involves recycling breeding material back into the crossing block as quickly as a breeder can determine that a genotype is above average in breeding value for a desired quantitative trait. Rapid generation advancement, widely known as “speed breeding” ( Watson et al, 2018 ), has been predominantly reported in Fabaceae species for recombinant inbred line production for molecular mapping and QTL discovery ( Lulsdorf and Banniza, 2018 ; Uz Zaman et al, 2019 ; Atieno et al, 2021 ; Dadu et al, 2021 ; Taylor et al, 2021 ). Another practical use of accelerated life cycling is to achieve rapid out-of-season turnover of promising breeding germplasm.…”

“…Based on the principles of single seed descent (Goulden, 1939;Brim, 1966), plants are grown under controlled conditions designed to reduce vegetative biomass partitioning and prioritize reproductive speed. A combination of photoperiod extension, late-spring temperatures, light wavelength optimization, 1 https://www.ipcc.ch/ar6-syr/ and precocious germination technology enable 50 to 60-day lifecycle completion year-round for chickpea, irrespective of the field flowering phenology (Croser et al, 2016;Atieno et al, 2021). Harnessing out-of-season accelerated generation turnover in combination with complementary tools such as marker-assisted selection (MAS) enables rapid identification and culling of lines not homozygous for a desired trait.…”

“…Accelerated Single Seed Descent (aSSD) F 2:4 F 2 seeds (n = 186 individuals) were received at UWA in October 2016 for accelerated single seed descent (aSSD) as applied in Atieno et al (2021). Two weeks after emergence, leaves were sampled and couriered to SARDI for MAS.…”