Search

SUMMARY: 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. Significance Statement: Integrated genomic strategy provides novel insights into the transcriptional regulatory role of functional allele and haplotype delineated in a MATE gene selected during Cicer domestication, in regulating varied seed color of chickpea. [ABSTRACT FROM AUTHOR]

Copyright of Plant Journal is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

SUMMARY: The advent of the pangenome era has unraveled previously unknown genetic variation existing within diverse crop plants, including rice. This untapped genetic variation is believed to account for a major portion of phenotypic variation existing in crop plants. However, the use of conventional single reference‐guided genotyping often fails to capture a large portion of this genetic variation leading to a reference bias. This makes it difficult to identify and utilize novel population/cultivar‐specific genes for crop improvement. Thus, we developed a Rice Pangenome Genotyping Array (RPGA) harboring probes assaying 80K single‐nucleotide polymorphisms (SNPs) and presence–absence variants spanning the entire 3K rice pangenome. This array provides a simple, user‐friendly and cost‐effective (60–80 USD per sample) solution for rapid pangenome‐based genotyping in rice. The genome‐wide association study (GWAS) conducted using RPGA‐SNP genotyping data of a rice diversity panel detected a total of 42 loci, including previously known as well as novel genomic loci regulating grain size/weight traits in rice. Eight of these identified trait‐associated loci (dispensable loci) could not be detected with conventional single reference genome‐based GWAS. A WD repeat‐containing PROTEIN 12 gene underlying one of such dispensable locus on chromosome 7 (qLWR7) along with other non‐dispensable loci were subsequently detected using high‐resolution quantitative trait loci mapping confirming authenticity of RPGA‐led GWAS. This demonstrates the potential of RPGA‐based genotyping to overcome reference bias. The application of RPGA‐based genotyping for population structure analysis, hybridity testing, ultra‐high‐density genetic map construction and chromosome‐level genome assembly, and marker‐assisted selection was also demonstrated. A web application (http://www.rpgaweb.com) was further developed to provide an easy to use platform for the imputation of RPGA‐based genotyping data using 3K rice reference panel and subsequent GWAS. Significance Statement: RPGA is a vital tool for diverse genomics‐assisted breeding applications and accelerated crop improvement in rice, as it provides an efficient pangenome‐based genotyping solution to overcome reference bias imposed by conventional single reference genome‐based genotyping strategies. [ABSTRACT FROM AUTHOR]