Stable heat tolerance QTLs in an inter-specific RILs population in chickpea

What is it about?

Manuscript Summary: Chickpea (Cicer arietinum L.), originated from Southeastern Turkey, is a self-pollinated diploid (2n = 2x = 16) crop having genome size of 738 Mb (Varshney et al. 2013). Among chickpea growing countries, India alone adds to about 70% of the world’s total production and ranks first in terms of production and productivity. Chickpea seeds have high amount of carbohydrates (around 60%) and protein (20–22%). It also contains essential amino acids, vitamins, minerals, and dietary fiber, which helps to improve insulin secretion and control blood sugar levels. Due to relatively low levels of polymorphism between cultivated chickpea genotypes, inter-specific crosses between C. arietinum and C. reticulatum have been the prime focus for genetic studies of agronomic traits (Kushwah et al. 2021). In spite of its economic importance and its role in human health, productivity has not been increased that much to meet the current demands. The sluggish pace of productivity is due to several abiotic and biotic constraints challenging the crop. Among abiotic stresses, heat is considered as one of the major constraints that affects the chickpea production. The amount of polymorphism in an inter-specific mapping population varied from 16% to 36%, whereas 9.5% only in an intra-specific mapping population. High-resolution genetic linkage maps can also be constructed by exploiting the inter-specific polymorphisms between C. arietinum and C. reticulatum. Variation detection based on SNPs has also shown the similar trends. Thus, an inter-specific mapping population from a cross between GPF 2 (C. arietinum) and ILWC 292 (C. reticulatum) has been used in the present study to identify the key genomic regions of heat tolerance related traits using ddRAD-seq based genotyping and phenotyping in contrasting environmental conditions. Chickpea cultivar GPF2 is a semi erect, medium tall cultivar released by Punjab Agricultural University, Ludhiana, Punjab and recommended for cultivation in Punjab state and in North Western Plains Zone of India. Another parent of RILs, ILWC292 (C. reticulatum) is the wild species of chickpea having semi prostrate growth habit. A total of 187 recombinant inbred lines (RILs) segregating for heat tolerance related traits from an inter-specific cross of cultivar GPF 2 (heat tolerant) × C. reticulatum acc ILWC 292 (heat sensitive) developed using single seed descent method. The RIL population along with parents was planted during winter’s season of 2017–18 in alpha lattice design (17 × 12) under timely-sown (November-April) and late-sown (January-May) conditions with three replications at two locations, i.e., Ludhiana and Faridkot. The late-sown chickpea was exposed to terminal heat stress because the conserved soil moisture recedes as the season progresses and the temperature rises. Thus, heat tolerance related traits have been studied in late-sown irrigated condition, using the timely-sown irrigated condition as a control. During the screening of heat tolerance, irrigation was provided to avoid the confounding effect of drought stress. The daily maximum temperatures for late-sown as well as timely-sown conditions during the reproductive phase at both the locations (Ludhiana and Faridkot) were recorded. Phenotypic data were collected for a total of 13 heat tolerance related traits. This study illustrated the presence of significant differences in inter-specific RIL population and its parents for yield and yield contributing traits and physiological traits in late-sown as compared to timely-sown condition. Reduction in seed yield during heat stress could be associated with low pollen viability in the RILs. A total of 28 QTLs at Ludhiana and 23 QTLs at Faridkot location were identified for 13 traits using SNP genotyping by ddRAD-Seq and BLUPs in the RIL population evaluated under timely-sown and late-sown conditions. Out of these, 13 stable QTLs for 7 traits were identified at both the locations. The stable QTLs for days to germination have been reported first time in the present study. The stable QTLs for flowering suggesting that these loci confer flowering time in chickpea and early flowering has an advantage of more pod setting before the occurrence of heat stress due to comparatively longer reproductive phase. Four QTL clusters containing QTLs for multiple traits identified on the same genomic region at both locations which would be the prime target in breeding programme for improving heat stress tolerance in chickpea. References: Kushwah A, Bhatia D, Singh G, Singh I, Bindra S, Vij S, et al (2021) Phenotypic evaluation of genetic variability and selection of yield contributing traits in chickpea recombinant inbred line population under high temperature stress. Physiology and Molecular Biology of Plants. 27(4):747–767 Varshney RK, Mohan SM, Gaur PM et al (2013) Achievements and prospects of genomics-assisted breeding in three legume crops of the semi-arid tropics. Biotechnology Advances. 10:1016–1022

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Why is it important?

In spite of its economic importance and its role in human health, chickpea productivity has not been increased that much to meet the current demands due to several abiotic constraints. Among these, heat is considered as one of the major constraints that affects the chickpea production. Stable QTLs identified in an inter-specific RILs population between C. arietinum and C. reticulatum which can be used in marker assisted breeding for heat tolerance.

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