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全基因组和泛基因组分析揭示了来自斯瓦伦的一个新培育野生稻品系中NBS-LRR基因的丰富变异。

Genome-wide and pan-genomic analysis reveals rich variants of NBS-LRR genes in a newly developed wild rice line from Swallen.

作者信息

Shivute Fimanekeni Ndaitavela, Zhong Yi, Wu Jinwen, Bao Yueming, Wang Wei, Liu Xiangdong, Lu Zijun, Yu Hang

机构信息

State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China.

Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China.

出版信息

Front Plant Sci. 2024 Apr 8;15:1345708. doi: 10.3389/fpls.2024.1345708. eCollection 2024.

DOI:10.3389/fpls.2024.1345708
PMID:38650702
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11033514/
Abstract

INTRODUCTION

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 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 (OA), 2 (OG) and 18 (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 Swallen that may provide a new germplasm for rice resistance breeding.

摘要

引言

宽叶野生稻是一种异源四倍体多年生野生稻，含有CCDD基因组，可能蕴藏着丰富遗传资源的有利基因。

方法

我们实验室从宽叶野生稻培育出一个新的野生稻品系华野5号。采用全基因组重测序和泛基因组分析来分析其基因组变异和新基因。

结果与讨论

与亚洲栽培稻相比，检测到超过一千万个基因组变异。在变异基因中，分别有724、197和710个基因编码蛋白激酶、合成酶和转录因子。共有353、131和135个变异基因分别与形态性状、生理性状、抗性或耐受性相关。共检测到62个NBS-LRR基因，其中11个NBS-LRR基因在叶鞘和成熟茎中表达，26个在幼根和成熟根中表达。通过整合8个（OA）、2个（OG）和18个（OL）种质构建了具有CCDD基因组的野生稻物种的泛基因组序列。共揭示了28个非参考NBS-LRR基因，其中7个主要在成熟根中表达。本研究表明宽叶野生稻具有丰富的DNA变异，可为水稻抗性育种提供新的种质资源。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ad4d/11033514/2021322c72a8/fpls-15-1345708-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ad4d/11033514/695a4d43d004/fpls-15-1345708-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ad4d/11033514/388047a66345/fpls-15-1345708-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ad4d/11033514/29508fbdadc5/fpls-15-1345708-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ad4d/11033514/38dc980bee78/fpls-15-1345708-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ad4d/11033514/77131e7416ca/fpls-15-1345708-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ad4d/11033514/cc8e8abfd6b3/fpls-15-1345708-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ad4d/11033514/2021322c72a8/fpls-15-1345708-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ad4d/11033514/695a4d43d004/fpls-15-1345708-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ad4d/11033514/388047a66345/fpls-15-1345708-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ad4d/11033514/29508fbdadc5/fpls-15-1345708-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ad4d/11033514/38dc980bee78/fpls-15-1345708-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ad4d/11033514/77131e7416ca/fpls-15-1345708-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ad4d/11033514/cc8e8abfd6b3/fpls-15-1345708-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ad4d/11033514/2021322c72a8/fpls-15-1345708-g007.jpg

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