数字农科院2.0

Polymorphism analysis of the chloroplast and mitochondrial genomes in soybean

文献类型： 外文期刊

作者： Yanlei Yue;Jiawen Li;Xuegang Sun;Zhen Li;Bingjun Jiang

作者机构：

关键词： Chloroplast genome;Haplotype, mitochondrial heterozygosity;Mitochondrial genome;Soybean

期刊名称： BMC Plant Biology

ISSN： 1471-2229

年卷期： 2023 年 23 卷 1 期

页码：

收录情况： SCIE（2023版）

摘要： Background: Soybean is an important protein- and oil-rich crop throughout the world. Much attention has been paid to its nuclear genome, which is bi-parentally inherited and associated with many important agronomical traits. However, less is known about the genomes of the semi-autonomous and essential organelles, chloroplasts and mitochondria, of soybean. Results: Here, through analyzing the polymorphisms of these organelles in 2580 soybean accessions including 107 wild soybeans, we found that the chloroplast genome is more variable than the mitochondrial genome in terms of variant density. Consistent with this, more haplotypes were found in the chloroplast genome (44 haplotypes) than the mitochondrial genome (30 haplotypes). These haplotypes were distributed extremely unevenly with the top two haplotypes (CT1 and CT2 for chloroplasts, MT1 and MT2 for mitochondria) accounting for nearly 70 and 18% of cultivated soybean accessions. Wild soybeans also exhibited more diversity in organelle genomes, harboring 32 chloroplast haplotypes and 19 mitochondrial haplotypes. However, only a small percentage of cultivated soybeans shared cytoplasm with wild soybeans. In particular, the two most frequent types of cytoplasm (CT1/MT1, CT2/MT2) were missing in wild soybeans, indicating that wild soybean cytoplasm has been poorly exploited during breeding. Consistent with the hypothesis that soybean originated in China, we found that China harbors the highest cytoplasmic diversity in the world. The geographical distributions of CT1–CT3 and MT1–MT3 in Northeast China were not significantly different from those in Middle and South China. Two mitochondrial polymorphism sites, p.457333 (T > C) and p.457550 (G > A), were found to be heterozygous in most soybeans, and heterozygosity appeared to be associated with the domestication of cultivated soybeans from wild soybeans, the improvement of landraces to generate elite cultivated soybeans, and the geographic adaptation of soybean. Conclusions: The haplotypes of thousands of soybean cultivars should be helpful in evaluating the impact of cytoplasm on soybean performance and in breeding cultivars with the desired cytoplasm. Mitochondrial heterozygosity might be related to soybean adaptation, and this hypothesis needs to be further investigated.

分类号：

  • 相关文献

[1]Comparative Genomics of Bryopsis hypnoides: Structural Conservation and Gene Transfer Between Chloroplast and Mitochondrial Genomes. Ziwen Liu,Xiao Fan,Yukun Wu,Wei Zhang,Xiaowen Zhang,Dong Xu,Yitao Wang,Ke Sun,Wei Wang,Naihao Ye. 2025

[2]The Complete Chloroplast Genome Of B.iondia Insignis Tsiang (Apocynaceae). Zhang, Rui,Guan, Min. 2019

[3]Comparative Analysis Of The Complete C.hloroplast Genome Of Four E ndangered Herbals Of Notopterygium. Yang, Jiao,Yue, Ming,Niu, Chuan,Ma, Xiong-Feng,Li, Zhong-Hu. 2017

[4]Comparative Chloroplast Genomics Of Gossypium S.pecies: Insights Into Repeat S equence Variations And Phylogeny. Zhou, Xiao-Jian,Zhang, Wen-Sheng,Wu, Ying,Zhou, Ke-Hai,Wu, Ying,Ren, Zhong-Ying,Pei, Xiao-Yu,Ma, Xiong-Feng,Li, Wei,Li, Zhong-Hu,He, Kun-Lun,Yang, Dai-Gang,Liu, Yan-Gai,Liu, Fang. 2018

[5]Assessing high-resolution melt curve analysis for accurate detection of DNA polymorphisms in the chloroplast gene accD of Crucifer species. Yan, Gui-xin,Wu, Xiao-ming,Li, Dan,Zeng, Chang-li,Lv, Pei-jun,Gao, Gui-zhen,Chen, Bi-yun,Xu, Kun,Lv, Xiao-dan,Zeng, Chang-li.

[6]The complete chloroplast genome of Arabidopsis lyrata. Wu, Zhiqiang,Gu, Cuihua,Tembrock, Luke R.,Sun, Cheng. 2016

[7]The complete chloroplast genome sequence of Chinese wild grape Vitis amurensis (Vitaceae: Vitis L.). Xie, Haikun,Jiao, Jian,Fan, Xiucai,Zhang, Ying,Jiang, Jianfu,Sun, Haisheng,Liu, Chonghuai.

[8]Sequencing of chloroplast genome using whole cellular DNA and Solexa sequencing technology. Wu, Jian,Liu, Bo,Cheng, Feng,Wang, Xiao-Wu,Ramchiary, Nirala,Choi, Su Ryun,Lim, Yong Pyo. 2012

[9]Comparative Bioinformatics Analysis of the Chloroplast Genomes of a Wild Diploid Gossypium and Two Cultivated Allotetraploid Species. Farshid Talat ,Kunbo Wang. 2015

[10]Complete chloroplast genome sequence of rapeseed (Brassica napus L.) and its evolutionary implications. Hu, Zhi-Yong,Hua, Wei,Huang, Shun-Mou,Wang, Han-Zhong,Hu, Zhi-Yong,Hua, Wei,Huang, Shun-Mou,Wang, Han-Zhong.

[11]The Complete Chloroplast Genome Sequences of Eight Fagopyrum Species: Insights Into Genome Evolution and Phylogenetic Relationships. Yu Fan,Ya’nan Jin,Mengqi Ding,Yu Tang,Jianping Cheng,Kaixuan Zhang,Meiliang Zhou. 2021

[12]A Phylogenetic Analysis Of Chloroplast G.enomes Elucidates The Relationships O f The Six Economically Important Brassica Species Comprising The Triangle Of U. Li, PR, Zhang, SJ, Li, F, Zhang, SF, Zhang, H, Wang, XW, Sun, RF, Bonnema, G, Borm, TJA. 2017

[13]Chloroplast Dna Markers For Echinochloa T.axa. Zhang, JP, Fu, F, Liu, C, Lin, ZX, Wang, YY, Ye, CY, Lu, YL. 2017

[14]Comprehensive Comparative Analysis and Development of Molecular Markers for Dianthus Species Based on Complete Chloroplast Genome Sequences. Lin S.,Liu J.,He X.,Wang J.,Wang Z.,Zhang X.,Bao M.,Fu X.. 2022

[15]The complete chloroplast genome of Desmodium uncinatum (Fabaceae). Dengxia Yi,Wenbo Jiang,Lin Ma,Yongzhen Pang. 2021

[16]The complete chloroplast genome of Bromus biebersteinii. Wenxuan Du,Junfeng Yang,Yongzhen Pang. 2021

[17]Chloroplast Genome Evolution in Four Montane Zingiberaceae Taxa in China. Qian Yang,Gao Fei Fu,Zhi Qiang Wu,Li Li,Jian Li Zhao,Qing Jun Li. 2022

[18]Comparative and Phylogenetic Analysis of Complete Chloroplast Genomes in Leymus (Triticodae, Poaceae). Wu Z.,Tian C.,Yang Y.,Li Y.,Liu Q.,Li Z.,Jin K.. 2022

[19]The complete chloroplast genome of Agropyron desertorum (Fisch. ex Link) Schult. Junfeng Yang,Wenxuan Du,Yongzhen Pang. 2021

[20]Analysis of codon usage patterns of the chloroplast genome in Delphinium grandiflorum L. reveals a preference for AT-ending codons as a result of major selection constraints. Huirong Duan,Qian Zhang,Chunmei Wang,Fang Li,Fuping Tian,Yuan Lu,Yu Hu,Hongshan Yang,Guangxin Cui. 2021

作者其他论文 更多>>