Abstract：
Seed color is one of the key target traits of domestication and artificial selection in chickpeas due to its implications on consumer preference and market value. The complex seed color trait has been well dissected in several crop species; however, the genetic mechanism underlying seed color variation in chickpea remains poorly understood. Here, we employed an integrated genomics strategy involving QTL mapping, high-density mapping, map-based cloning, association analysis, and molecular haplotyping in an inter-specific RIL mapping population, association panel, wild accessions, and introgression lines (ILs) of Cicer gene pool. This delineated a MATE gene, CaMATE23, encoding a Transparent Testa (TT) and its natural allele (8-bp insertion) and haplotype underlying a major QTL governing seed color on chickpea chromosome 4. Signatures of selective sweep and a strong purifying selection reflected that CaMATE23, especially its 8-bp insertion natural allelic variant, underwent selection during chickpea domestication. Functional investigations revealed that the 8-bp insertion containing the third cis-regulatory RY-motif element in the CaMATE23 promoter is critical for enhanced binding of CaFUSCA3 transcription factor, a key regulator of seed development and flavonoid biosynthesis, thereby affecting CaMATE23 expression and proanthocyanidin (PA) accumulation in the seed coat to impart varied seed color in chickpea. Consequently, overexpression of CaMATE23 in Arabidopsis tt12 mutant partially restored the seed color phenotype to brown pigmentation, ascertaining its functional role in PA accumulation in the seed coat. These findings shed new light on the seed color regulation and evolutionary history, and highlight the transcriptional regulation of CaMATE23 by CaFUSCA3 in modulating seed color in chickpea. The functionally relevant InDel variation, natural allele, and haplotype from CaMATE23 are vital for translational genomic research, including marker-assisted breeding, for developing chickpea cultivars with desirable seed color that appeal to consumers and meet global market demand.
摘要：
籽色是鹰嘴豆驯化和人工选择的关键目标性状之一，因为它对消费者的偏好和市场价值有影响。复杂的种子颜色性状已经在几种作物中得到了很好的解剖；然而，鹰嘴豆种子颜色变异的遗传机制仍然知之甚少。这里,我们采用了涉及QTL定位的综合基因组学策略，高密度测绘，基于地图的克隆，关联分析,和特异性RIL作图群体中的分子单倍型分型，协会小组，野生物种,和Cicer基因库的基因渗入系(ILs)。这描绘了一个MATE基因，CaMATE23，编码透明Testa（TT）及其天然等位基因（8bp插入）和单倍型，是鹰嘴豆4号染色体上控制种子颜色的主要QTL。选择性扫描和强纯化选择的签名反映了CaMATE23，尤其是其8bp插入天然等位基因变体，在鹰嘴豆驯化过程中进行选择。功能研究表明，在CaMATE23启动子中包含第三个顺式调节RY基序元件的8bp插入对于增强CaFUSCA3转录因子的结合至关重要，种子发育和类黄酮生物合成的关键调节剂，从而影响CaMATE23的表达和原花青素（PA）在种皮中的积累，从而赋予鹰嘴豆不同的种子颜色。因此,CaMATE23在拟南芥tt12突变体中的过表达部分恢复了种子颜色表型为棕色色素沉着，确定其在种皮中PA积累中的功能作用。这些发现为种子颜色调节和进化史提供了新的启示，并强调了CaFUSCA3对鹰嘴豆种子颜色的转录调节。功能相关的InDel变异，天然等位基因，来自CaMATE23的单倍型对翻译基因组研究至关重要，包括标记辅助育种，用于开发具有理想种子颜色的鹰嘴豆品种，以吸引消费者并满足全球市场需求。
