Genome-wide and pan-genomic analysis reveals rich variants of NBS-LRR genes in a newly developed wild rice line from Oryza alta Swallen
文献类型： 外文期刊
作者： Shivute, Fimanekeni Ndaitavela 1 ; Zhong, Yi 1 ; Wu, Jinwen 1 ; Bao, Yueming 1 ; Wang, Wei 1 ; Liu, Xiangdong 1 ; Lu, Zijun 1 ; Yu, Hang 4 ;
作者机构： 1.South China Agr Univ, State Key Lab Conservat & Utilizat Subtrop Agrobio, Guangdong Lab Lingnan Modern Agr, Guangzhou, Peoples R China
2.South China Agr Univ, Guangdong Prov Key Lab Plant Mol Breeding, Guangzhou, Peoples R China
3.South China Agr Univ, Coll Agr, Guangzhou, Peoples R China
4.Guangdong Acad Agr Sci, Rice Res Inst, Guangzhou, Peoples R China
关键词： germplasm; wild rice; Oryza alta swallen; genome sequencing; pan-genome
期刊名称：FRONTIERS IN PLANT SCIENCE （ 影响因子：5.6； 五年影响因子：6.8 ）
ISSN： 1664-462X
年卷期： 2024 年 15 卷
页码：
收录情况： SCI
摘要： Introduction: Oryza alta Swallen is an allotetraploid perennial wild rice and contains CCDD genome, which may harbor favorable genes for the enrichment of genetic resource. Methods: A new wild rice line, Huaye 5, was developed from Oryza alta Swallen in our lab. Whole genome re-sequencing and pan-genomic analysis were employed to analyze its genomic variations and novel genes. Results and Discussion: More than ten million genomic variations were detected when compared with Asian cultivar. Among the variational genes, 724, 197 and 710 genes coded protein kinase, synthetase and transcription factor, respectively. A total of 353, 131 and 135 variational genes were associated with morphological trait, physiological trait, resistance or tolerance, respectively. A total of 62 were NBS-LRR genes were detected, in which 11 NBS-LRR genes expressed in sheath and mature stem, and 26 expressed in young and mature roots expressed. The pan-genome sequences of wild rice species with CCDD genome were constructed by integrating 8 Oryza alta (OA), 2 Oryza grandiglumis (OG) and 18 Oryza latifolia (OL) accessions. A total of 28 non-reference NBS-LRR genes were revealed, and 7 of which were mainly expressed in mature roots. This research demonstrated rich DNA variation in the Oryza alta Swallen that may provide a new germplasm for rice resistance breeding.
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