A superior gene allele involved in abscisic acid signaling enhances drought tolerance and yield in chickpea

Abstract

Identifying potential molecular tags for drought tolerance is essential for achieving higher crop productivity under drought stress. We employed an integrated genomics-assisted breeding and functional genomics strategy involving association mapping, fine mapping, map-based cloning, molecular haplotyping and transcript profiling in the introgression lines (ILs)- and near isogenic lines (NILs)-based association panel and mapping population of chickpea (Cicer arietinum). This combinatorial approach delineated a bHLH (basic helix-loop-helix) transcription factor, CabHLH10 (Cicer arietinum bHLH10) underlying a major QTL, along with its derived natural alleles/haplotypes governing yield traits under drought stress in chickpea. CabHLH10 binds to a cis-regulatory G-box promoter element to modulate the expression of RD22 (responsive to desiccation 22), a drought/ABA-responsive gene (via a trans-expression QTL), and two strong yield-enhancement photosynthetic efficiency (PE) genes. This, in turn, upregulates other downstream drought-responsive and abscisic acid signaling genes, as well as yield-enhancing PE genes, thus increasing plant adaptation to drought with reduced yield penalty. We showed that a superior allele of CabHLH10 introgressed into the NILs improved root and shoot biomass and PE, thereby enhancing yield and productivity during drought without compromising agronomic performance. Furthermore, overexpression of CabHLH10 in chickpea and Arabidopsis (Arabidopsis thaliana) conferred enhanced drought tolerance by improving root and shoot agro-morphological traits. These findings facilitate translational genomics for crop improvement and the development of genetically-tailored, climate-resilient, high-yielding chickpea cultivars.

Phenotypic and Genetic Characterization of a Near-Isogenic Line Pair: Insights into Flowering Time in Chickpea.

“…The sequencing data from the pair of NILs revealed a 99.97% identity of the read positions, with variations mainly observed in speci c regions, as expected [41]. This level of genomic identity is consistent with values from other legume studies involving NILs, including chickpea, where reported identities range between 90-99% [50,72,73]. The observed residual heterozygosity for each NIL is ~ 0.05%, falling below the theoretical 0.098% expected for 11 generations of self-fertilizing lines.…”

Functional allele of a MATE gene selected during domestication modulates seed color in chickpea

“…Total RNA was isolated from the shoots, roots, flowers, and seed coat tissues (100–200 mg) of gray‐ and dark seed‐colored introgression lines (ILs; Thakro et al., 2023) and mapping parental accessions (ICC 4958 and ICC 17160) using TRIzol (Sigma‐Aldrich) reagent and RNeasy MinElute Cleanup Kit (Qiagen, USA/), following manufacturer's instructions. Gene‐specific primer pairs were designed using Primer Express (v3.0) with default parameters (Applied Biosystems, Foster City, CA), and they were synthesized (Sigma‐Aldrich) (Table S14).…”

Functions of Basic Helix–Loop–Helix (bHLH) Proteins in the Regulation of Plant Responses to Cold, Drought, Salt, and Iron Deficiency: A Comprehensive Review

“…Similarly, CabHLH10 specifically binds to the G-box elements in the promoter of CaRD22, a dehydration-and ABA-responsive gene, and then enhances its expression to confer ABA-dependent drought tolerance as well as enhance yield/productivity in Cicer arietinum. 64 CibHLH96 binds to the CiFD promoter and activates its expression to regulate drought-induced flowering in citrus. [70][71][72]74,76,77,79 In Zoysia japonica, ZjICE1/2 directly binds to the MYC motifs in the promoter of ZjDREB1, resulting in elevated expression and increased drought stress tolerance.…”

“…Li et al recently identified AhbHLH112 can activates AhPOD transcription via direct binding with G/E-box elements in peanut. Similarly, CabHLH10 specifically binds to the G-box elements in the promoter of CaRD22 , a dehydration- and ABA-responsive gene, and then enhances its expression to confer ABA-dependent drought tolerance as well as enhance yield/productivity in Cicer arietinum . CibHLH96 binds to the CiFD promoter and activates its expression to regulate drought-induced flowering in citrus. − ,,,, In Zoysia japonica , ZjICE1/2 directly binds to the MYC motifs in the promoter of ZjDREB1 , resulting in elevated expression and increased drought stress tolerance. , In rice, OsbHLH057 binds to the AATCA cis -element of the Os2H16 promoter and then promotes its expression .…”