Identification of Candidate Genes for Winter Hardiness in Chickpea

Abstract

Chickpea (Cicer arietinum L.) is a highly profitable crop due to its high dietary protein content and fiber, critical minerals, and excellent capability to fix atmospheric nitrogen, especially in low-cost food production systems. If chickpea experienced low-temperature stress (0 – 15°C) during the reproductive stage, severe loss of flowers and pods would occur to hinder its yield potential by 30 – 40%. Winter-sown chickpeas, however, suffer from cold stress during their vegetative stages. The reproductive period is significant for agricultural yields, during which low temperature stress results in flower abortion, pollen, and ovule infertility, disrupts fertilization, decreases pod set, delays seed filling, and eventually, reduces seed size and yield. In the development of chickpea cultivars, four general objectives are identified: increasing grain yield, optimizing nutritional quality, having long-term adaptation, and enhancing resistance to biotic and abiotic stresses. Use of the modern breeding technologies is projected to result in significant increases in agricultural production in short period. Integration of modern genomic resources with conventional breeding efforts is expected to result in more climate-resilient and/or smart chickpea varieties in a shorter period. In this study, we aimed to identify the candidate gene(s) and develop ready-used genomic tools for chickpea winter hardiness that are used for cloning of the genes controlling chickpea winter hardiness and for chickpea breeding in winter hardiness. An interspecific recombinant inbred line (RIL) population was used for this study that was derived from a cross between ICC 4958, a cold-sensitive desi-type (C. arienitum L.), and PI 489777, a cold-tolerant wild relative (C. reticulatum L.). The candidate genes for winter hardiness were identified by integrative analysis of chickpea transcriptomes of the RILs that were subjected to a long and cold winter with their winter hardiness performance, followed by physically mapping the potential candidate genes to the intervals of the winter hardiness QTLs previously mapped by QTL mapping. Eighty-five common genes were found after comparative analysis of the genes that significantly differentially expressed between winter hardiness RILs and sensitive RILs (differentially expressed genes, DEGs) and the genes whose expressions were significantly correlated with winter hardiness. When these 85 common genes were aligned to the chickpea reference genome, seven of them were mapped to the interval of a major winter hardiness QTL previously mapped on chromosome 3. Furthermore, these seven genes were found to be involved in the glycerolipid metabolism (ATS1) in Arabidopsis that plays important roles in plant cold tolerance. Therefore, they were selected as the most promising candidate genes for winter hardiness in chickpea. Single nucleotide polymorphism (SNP) markers were developed for the interval of the winter hardiness QTL. These candidate genes and SNP markers have laid a foundation for cloning of the gene controlling winter hardiness in chickpea and provide molecular tools useful for enhanced chickpea breeding in winter hardiness.