Developing functional molecular tags from the cis-regulatory sequence components of genes is vital for their deployment in efficient genetic dissection of complex quantitative traits in crop plants including chickpea. The current study identified 431,194 conserved non-coding SNP (CNSNP) from the cis-regulatory element regions of genes which were annotated on a chickpea genome. These genome-wide CNSNP marker resources are made publicly accessible through a user-friendly web-database (http://www.cnsnpcicarbase.com). The CNSNP-based quantitative trait loci (QTL) and expression QTL (eQTL) mapping and genome-wide association study (GWAS) were further integrated with global gene expression landscapes, molecular haplotyping, and DNA-protein interaction study in the association panel and recombinant inbred lines (RIL) mapping population to decode complex genetic architecture of one of the vital seed yield trait under drought stress, drought yield index (DYI), in chickpea. This delineated two constituted natural haplotypes and alleles from a histone H3 protein-coding gene and its transcriptional regulator NAC transcription factor (TF) harboring the major QTLs and trans-acting eQTL governing DYI in chickpea. The effect of CNSNPs in TF-binding cis-element of a histone H3 gene in altering the binding affinity and transcriptional activity of NAC TF based on chromatin immunoprecipitation-quantitative PCR (ChIP-qPCR) assay was evident. The CNSNP-led promising molecular tags scanned will essentially have functional significance to decode transcriptional gene regulatory function and thus can drive translational genomic analysis in chickpea.

中文翻译：

---

全基因组的顺式调控信号调节农艺性状，如鹰嘴豆的干旱产量指数（DYI）。

从基因的顺式调控序列成分中开发功能性分子标签，对于它们在包括鹰嘴豆在内的农作物中有效定量解剖复杂数量性状的部署至关重要。目前的研究从鹰嘴豆基因组中注释的基因的顺式调控元件区域中鉴定出431,194个保守的非编码SNP（CNSNP）。这些全基因组的CNSNP标记资源可通过用户友好的Web数据库（http://www.cnsnpcicarbase.com）。基于CNSNP的数量性状基因座（QTL）和表达QTL（eQTL）定位以及全基因组关联研究（GWAS）在关联面板中进一步整合了全球基因表达格局，分子单体型和DNA-蛋白质相互作用研究，并进行了重组鹰嘴豆的近交系（RIL）作图群体，以解码干旱胁迫下重要种子产量性状之一（干旱产量指数（DYI））的复杂遗传结构。这描绘了由组蛋白H3蛋白编码基因及其转录调节子NAC转录因子（TF）组成的两个自然的单倍型和等位基因，该基因包含鹰嘴豆的主要QTL和控制DYI的反式eQTL。CNSNPs在TF结合顺式中的作用染色质免疫沉淀-定量PCR（ChIP-qPCR）分析表明，组蛋白H3基因在改变NAC TF的结合亲和力和转录活性中是很明显的。扫描的CNSNP主导的有前途的分子标签将本质上具有解码转录基因调控功能的功能意义，因此可以推动鹰嘴豆的翻译基因组分析。