通过GWAS鉴定水稻果皮颜色的基因组位点

IF 1 4区 生物学 Q3 PLANT SCIENCES Indian Journal of Genetics and Plant Breeding Pub Date : 2022-02-25 DOI:10.31742/ijgpb.82.1.1
N. Rana, S. Kumawat, U. Singh, V. Singh, R. Deshmukh, T. Sharma, H. Sonah
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引用次数: 0

摘要

稻米果皮颜色是目前世界范围内关注的营养特征之一。在本研究中,进行了全基因组关联(GWAS)来鉴定控制水稻果皮颜色的基因座。一组1349269个SNPs和325份不同水稻材料的精确表型用于GWAS。材料可分为籼稻、粳稻、芳香型、aus型和混合型五个同工酶类群。GWAS在染色体5和7上分别鉴定了两个与水稻果皮颜色相关的重要基因座gPC5-1和gPC7-1。7号染色体上的SNPs与已知控制果皮颜色的具有功能特征的Os07g0211500(Rc基因)和与参与类黄酮合成途径的查尔酮合成酶2(OsCHS2)基因相似的Os07g 0214900共定位。这些标记上游和下游0.25Mbp的连锁不平衡分析表明,7号染色体上有三个强连锁区。更有趣的是,在5号染色体gPC5-1上鉴定的新基因座没有任何先前报道的基因同源物。因此,该基因座可以作为鉴定水稻果皮颜色新基因的基础。本文的研究结果将有助于理解水稻果皮颜色的遗传调控和基因组辅助育种。
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Identification of genomic loci governing pericarp colour through GWAS in rice (Oryza sativa L.)
Rice pericarp colour is one of the nutritional traits that is now gaining attention worldwide. In the present investigation, genome-wide association GWAS) was performed to identify loci governing pericarp colour in rice. A set of 1,349,269 SNPs and precise phenotyping across 325 diverse accessions of rice were used for the GWAS. The accessions belong to five rice isozyme classification groups viz., indica, japonica, aromatic, aus, and admix. The GWAS identified two significant loci gPC5-1and gPC7-1 on chromosomes, 5 and 7, respectively, associated with the pericarp colour in rice. The SNPs on chromosome 7 co-localized with the functionally characterized Os07g0211500 (Rc gene) known to control pericarp colour and Os07g0214900 which is similar to the Chalcone synthase 2(OsCHS2) gene involved in flavonoid synthesis pathway. Linkage disequilibrium analysis across 0.25 Mbp upstream and downstream of these markers suggested three strong linkage blocks on chromosome 7. More interestingly, the novel locus identified on chromosome 5 gPC5-1 does not harbor any homolog of previously reported genes. Therefore, the locus can serve as a basis for identifying a new gene for rice pericarp colour. The results presented here will be helpful to understand the genetic regulation of pericarp colour and for genomic-assisted breeding in rice.
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来源期刊
CiteScore
1.80
自引率
10.00%
发文量
0
审稿时长
6-12 weeks
期刊介绍: Advance the cause of genetics and plant breeding and to encourage and promote study and research in these disciplines in the service of agriculture; to disseminate the knowledge of genetics and plant breeding; provide facilities for association and conference among students of genetics and plant breeding and for encouragement of close relationship between them and those in the related sciences; advocate policies in the interest of the nation in the field of genetics and plant breeding, and facilitate international cooperation in the field of genetics and plant breeding.
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