Acta Agronomica Sinica ›› 2022, Vol. 48 ›› Issue (10): 2483-2493.doi: 10.3724/SP.J.1006.2022.12067
• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles Next Articles
SUN Bing-Rui(), PAN Da-Jian, LI Chen, JIANG Li-Qun, ZHANG Jing, LYU Shu-Wei, LIU Qing, MAO Xing-Xue, CHEN Wen-Feng(), FAN Zhi-Lan()
[1] | 何秀英, 周少川, 刘志霞, 刘传光. 广东省农业科学院常规水稻育种60年: 成就与展望. 广东农业科学, 2020, 47(11): 1-8. |
He X Y, Zhou S C, Liu Z X, Liu C G. Sixty year’s conventional rice breeding of Guangdong Academy of Agricultural Sciences: achievements and prospects. Guangdong Agric Sci, 2020, 47(11): 1-8. (in Chinese with English abstract) | |
[2] | 刘定富. 解密中国“水稻品种之最”. 种业商务网, 2021 [2021-07-15]. |
Liu D F. Deciphering China’s “Most rice varieties”. Seed Business Network, 2021 [2021-07-15]. https://www.chinaseed114.com/news/23/news_111858.html. (in Chinese) | |
[3] |
Yang X H, Xia X Z, Zhang Z Q, Nong B X, Zeng Y, Wu Y Y, Xiong F Q, Zhang Y X, Liang H F, Pan Y H, Dai G X, Deng G F, Li D T. Identification of anthocyanin biosynthesis genes in rice pericarp using PCAMP. Plant Biotechnol J, 2019, 17: 1700-1702.
doi: 10.1111/pbi.13133 |
[4] |
Sun J, Ma D R, Tang L, M H, Zhang G C, Wang W J, Song J Y, Li X, Liu Z M, Zhang W X, Xu Q, Zhou Y C, Wu J Z, Yamamoto T, Dai F, Lei Y, Li S, Zhou G, Zheng H K, Xu Z J, Chen W F. Population genomic analysis and de novo assembly reveal the origin of weedy rice as an evolutionary game. Mol Plant, 2019, 12: 632-647.
doi: 10.1016/j.molp.2019.01.019 |
[5] | Yang Z E, Ge X Y, Yang Z R, Qin W Q, Sun G F, Wang Z, Li Z, Liu J, Wu J, Wang Y, Lu L L, Wang P, Mo H J, Zhang X Y, Li F G. Extensive intraspecific gene order and gene structural variations in upland cotton cultivars. Nat Commun, 2019, 10: 2989. |
[6] |
Zhang Z, Li J W, Jamshed M, Shi Y Z, Liu A Y, Gong J W, Wang S F, Zhang J H, Sun F D, Jia F, Ge Q, Fan L Q, Zhang Z B, Pan J T, Fan S M, Wang Y L, Lu Q W, Liu R X, Deng X Y, Zou X Y, Jiang X, Liu P, Li P T, Iqbal M S, Zhang C Y, Zou J, Chen H, Tian Q, Jia X H, Wang B Q, Ai N J, Feng G L, Wang Y M, Hong M, Li S L, Lian W M, Wu B, Hua J P, Zhang C J, Huang J Y, Xu A X, Shang H H, Gong W K, Yuan Y L. Genome-wide quantitative trait loci reveal the genetic basis of cotton fibre quality and yield-related traits in a Gossypium hirsutum recombinant inbred line population. Plant Biotechnol J, 2020, 18: 239-253.
doi: 10.1111/pbi.13191 pmid: 31199554 |
[7] | Li R G, Song W, Wang B Q, Wang J H, Zhang D M, Zhang Q G, Li X H, Wei J F, Gao Z Y. Identification of a locus conferring dominant resistance to maize rough dwarf disease in maize. Sci Rep, 2018, 8: 3248. |
[8] |
Khanzada H K, Wassan G M, He H H, Mason A S, Keerio A A, Khanzada S, Faheem M, Solangi A M, Zhou Q H, Fu D H, Huang Y J. Differentially evolved drought stress indices determine the genetic variation of Brassica napus at seedling traits by genome-wide association mapping. J Adv Res, 2020, 24: 447-461.
doi: 10.1016/j.jare.2020.05.019 pmid: 32577311 |
[9] | Lu K, Wei L J, Li X L, Wang Y T, Wu J, Liu M, Zhang C, Chen Z Y, Xiao Z C, Jian H J, Cheng F, Zhang K, Du H, Cheng X C, Qu C M, Qian W, Liu L Z, Wang R, Zou Q Y, Ying J M, Xu X F, Mei J Q, Liang Y, Chai Y R, Tang Z L, Wan H F, Ni Y, He Y J, Lin N, Fan Y H, Sun W, Li N N, Zhou G, Zheng H K, Wang X W, Paterson A H, Li J N. Whole-genome resequencing reveals Brassica napus origin and genetic loci involved in its improvement. Nat Commun, 2019, 10: 1154. |
[10] |
Zhuang W J, Chen H, Yang M, Wang J P , Pandey M K , Zhang C, Chang W C, Zhang L S, Zhang X T, Tang R H, Garg V, Wang X J, Tang H B, Chow C N, Wang J P, Deng Y, Wang D P, Khan A W , Yang Q, Cai T C, Bajaj P , Wu K C, Guo B Z, Zhang X Y, Li J J, Liang F , Hu J, Liao B S, Liu S Y, Chitikineni A, Yan H S, Zheng Y X, Shan S H, Liu Q Z, Xie D Y, Wang Z Y, Khan S A, Ali N, Zhao C Z, Li X G, Luo Z L, Zhang S B, Zhuang R R, Peng Z , Wang S Y, Mamadou G, Zhuang Y H, Zhao Z F, Yu W C, Xiong F Q, Quan W P, Yuan M, Li Y, Zou H S, Xia H, Zha L, Fan J P, Yu J G, Xie W P, Yuan J Q, Chen K, Zhao S S, Chu W T, Yuting Y T, Sun P C, Meng F B, Zhuo T, Zhao Y H, Li C J, He G H, Zhao Y L, Wang C C, Kavikishor P B, Pan R L, Paterson A H, Wang X Y , Ming R. The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication. Nat Genet, 2019, 51: 865-876.
doi: 10.1038/s41588-019-0402-2 |
[11] | Yang M Y, Li G R, Wan H S, Li L P, Li J, Yang W Y, Pu Z J, Yang Z J, Yang E N. Identification of QTLs for stripe rust resistance in a recombinant inbred line population. Int J Mol Sci, 2019, 20: 3410. |
[12] |
Wu D P, Li D M, Zhao X, Zhan Y H, Teng W L, Qiu L J, Zheng H K, Li W B, Han Y P. Identification of a candidate gene associated with isoflflavone content in soybean seeds using genome-wide association and linkage mapping. Plant J, 2020, 104: 950-963.
doi: 10.1111/tpj.14972 |
[13] | Zhong C, Sun S L, Yao L L, Ding J J, Duan C X, Zhu Z D. 2 in soybean. Front Plant Sci, 2018, 9: 44. |
[14] |
Xu X W, Wei C X, Liu Q Y, Qu W Q, Qi X H, Xu Q, Chen X H. The major-effect quantitative trait locus Fnl7.1 encodes a late embryogenesis abundant protein associated with fruit neck length in cucumber. Plant Biotechnol J, 2020, 18: 1598-1609.
doi: 10.1111/pbi.13326 |
[15] |
Muntha S T, Zhang L L, Zhou Y F, Zhao X, Hu Z Y, Yang J H, Zhang M F. Phytochrome a signal transduction 1 and CONSTANS-LIKE 13 coordinately orchestrate shoot branching and flowering in leafy Brassica juncea. Plant Biotechnol J, 2019, 17: 1333-1343.
doi: 10.1111/pbi.13057 pmid: 30578711 |
[16] |
Cheng F, Sun R F, Hou X L, Zheng H K, Zhang F L, Zhang Y Y, Liu B, Liang J L, Zhuang M, Liu Y X, Liu D Y, Wang X B, Li P X, Liu Y M, Lin K, Bucher J, Zhang N W, Wang Y, Wang H, Deng J, Liao Y C, Wei K Y, Zhang X M, Fu L X, Hu Y Y, Liu J S, Cai C C, Zhang S J, Zhang S F, Li F, Zhang H, Zhang J F, Guo N, Liu Z Y, Liu J, Sun C, Ma Y, Zhang H J, Cui Y, Freeling M R, Borm T, Bonnema G, Wu J, Wang X W. Subgenome parallel selection is associated with morphotype diversification and convergent crop domestication in Brassica rapa and Brassica oleracea. Nat Genet, 2016, 48: 1218-1224.
doi: 10.1038/ng.3634 pmid: 27526322 |
[17] |
Chen D H, Ronald P C. A rapid DNA minipreparation method suitable for AFLP and other PCR applications. Plant Mol Biol Rep, 1999, 17: 53-57.
doi: 10.1023/A:1007585532036 |
[18] |
Landjeva S, Korzun V, Börner A. Molecular markers: actual and potential contributions to wheat genome characterization and breeding. Euphytica, 2007, 156: 271-296.
doi: 10.1007/s10681-007-9371-0 |
[19] |
Kozich J J, Westcott S L, Baxter N T, Highlander S K, Schloss P D. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeqIllumina sequencing platform. Appl Environment Microbiol, 2013, 79: 5112-5120.
doi: 10.1128/AEM.01043-13 |
[20] |
Price A L, Patterson N J, Plenge R M, Weinblatt M E, Shadick N A, Reich D. Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet, 2006, 38: 904-909.
doi: 10.1038/ng1847 |
[21] |
Koichiro T, Daniel P, Glen S, Masatoshi N, Sudhir K. MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol, 2011, 28: 2731-2739.
doi: 10.1093/molbev/msr121 pmid: 21546353 |
[22] |
Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol, 1987, 4: 406-425.
doi: 10.1093/oxfordjournals.molbev.a040454 pmid: 3447015 |
[23] |
Alexander D H, Novembre J, Lange K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res, 2009, 19: 1655-1664.
doi: 10.1101/gr.094052.109 pmid: 19648217 |
[24] |
de Hoon M J L D, Imoto S, Nolan J. Open source clustering software. Bioinformatics, 2004, 20: 1453-1454.
doi: 10.1093/bioinformatics/bth078 pmid: 14871861 |
[25] | 徐大勇, 钟环, 周峰, 陈庭木, 迟铭, 李健, 江玲, 万建民. 中粳水稻品种资源遗传多样性研究: III. 不同时期育成品种SSR多样性的比较分析. 浙江农业学报, 2011, 23: 8-14. |
Xu D Y, Zhong H, Zhou F, Chen T M, Chi M, Li J, Jiang L, Wan J M. Genetic diversity of mid-ripen japonica varieties: III. Comparison of variety diversity in different breeding periods with SSR markers. Acta Agric Zhejiangensis, 2011, 23: 8-14. (in Chinese with English abstract) | |
[26] | 齐永文, 张冬玲, 张洪亮, 王美兴, 孙俊立, 廖登群, 魏兴华, 裘宗恩, 汤圣祥, 曹永生, 王象坤, 李自超. 中国水稻选育品种遗传多样性及其近50年变化趋势. 科学通报, 2006, 51: 693-699. |
Qi Y W, Zhang D L, Zhang H L, Wang M X, Sun J L, Liao D Q, Wei X H, Qiu Z N, Tang S X, Cao Y S, Wang X K, Li Z C. Genetic diversity of Chinese rice breeding varieties and its changing trends in the past 50 years. Sci Bull, 51: 693-699. (in Chinese with English abstract) | |
[27] | 林世成, 闵绍楷. 中国水稻品种及其系谱. 上海: 上海科学技术出版社, 1991. pp 156-179. |
Lin S C, Min S K. Chinese Rice Varieties and Their Pedigree. Shanghai: Shanghai Scientific and Technical Publishers, 1991. pp 156-179. (in Chinese) | |
[28] |
Zhang J, Sun B R, Li C, Chen W F, Jiang L Q, Lyu S W, Fan Z L, Pan D J. Molecular diversity and genetic structure of wild rice accessions (Oryza rufifipogon Griff.) in Guangdong province, China, as revealed by SNP markers. Genet Resour Crop Evol, 2021, 68: 969-978.
doi: 10.1007/s10722-020-01038-8 |
[29] | Su W J, Wang L J, Lei J, Chai S S, Liu Y, Yang Y Y, Yang X S, Jiao C H. Genome-wide assessment of population structure and genetic diversity and development of a core germplasm set for sweet potato based on specific length amplified fragment (SLAF) sequencing. PLoS One, 2017, 12: e0172066. |
[30] | Fang H T, Liu H Y, Ma R S, Liu Y X, Li J N, Yu X Y, Zhang H Y, Yang Y L, Zhang G D. Genome-wide assessment of population structure and genetic diversity of Chinese Lou onion using specific length amplified fragment (SLAF) sequencing. PLoS One, 2020, 15: e0231753. |
[31] | Zhao X, Bao D F, Wang W, Zhang C J, Jing Y, Jiang H P, Qiu L J, Li W B, Han Y P. Loci and candidate gene identification for soybean resistance to Phytophthora root rot race 1 in combination with association and linkage mapping. Mol Breed, 2020, 40: 100. |
[32] | 孙建昌, 曹桂兰, 李亚非, 马静, 陈耀锋, 韩龙植. 水稻地方品种群体内的遗传多样性分析. 西北农林科技大学学报(自然科学版), 2011, 39: 145-158. |
Sun J C, Cao G L, Li Y F, Ma J, Chen Y F, Han L Z. Analysis of genetic diversity within populations of rice (Oryza sativa L.) landraces. J Northwest A&F Univ (Nat Sci Edn), 2011, 39: 145-158. (in Chinese with English abstract) | |
[33] |
Li M Z, Tian S L, Jin L, Zhou G Y, Li Y, Zhang Y, Wang T, Yeung C K L, Chen L, Ma J D, Zhang J B, Jiang A A, Li J, Zhou C W, Zhang J, Liu Y K, Sun X Q, Zhao H W, Niu Z X, Lou P, Xian L J, Shen X Y, Liu S Q, Zhang S H, Zhang M W, Zhu L, Shuai S R, Bai L, Tang G Q, Liu H F, Jiang Y Z, Mai M M, Xiao J, Wang X, Zhou Q, Wang Z Q, Stothard P, Xue M, Gao X L, Luo Z G, Gu Y R, Zhu H M, Hu X X, Zhao Y F, Plastow G S, Wang J Y, Jiang Z, Li K, Li N, Li X W, Li R Q. Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars. Nat Genet, 2013, 45: 1431-1438.
doi: 10.1038/ng.2811 |
[34] |
Rivera D, Prates I, Firneno J T J, Rodrigues M T, Caldwell J P, Fujita M K. Phylogenomics, introgression, and demographic history of South American true toads (Rhinella). Mol Ecol, 2021, 31: 978-992.
doi: 10.1111/mec.16280 |
[35] |
孙倩, 邹枚伶, 张辰笈, 江思容, Oliveira E J D, 张圣奎, 夏志强, 王文泉, 李有志. 基于SNP和InDel标记的巴西木薯遗传多样性与群体遗传结构分析. 作物学报, 2021, 47: 42-49.
doi: 10.3724/SP.J.1006.2021.04067 |
Sun Q, Zou M L, Zhang C J, Jiang S R, Oliveira E J D, Zhang S K, Xia Z Q, Wang W Q, Li Y Z. Genetic diversity and population structure analysis by SNP and InDel markers of cassava in Brazil. Acta Agron Sin, 2021, 47: 42-49. (in Chinese with English abstract)
doi: 10.3724/SP.J.1006.2021.04067 |
[1] | MA Yan-Song, LIU Zhang-Xiong, WEN Zi-Xiang, WEI Shu-Hong, YANG Chun-Ming, WANG Hui-Cai6, YANG Chun-Yan, LU Wei-Guo, XU Ran, ZHANG Wan-Hai, WU Ji-An, HU Guo-Hua, LUAN Xiao-Yan, FU . Effect of Population Structure on Prediction Accuracy of Soybean 100-Seed Weight by Genomic Selection MA Yan-Song1,2,13, LIU Zhang-Xiong1, WEN Zi-Xiang3, WEI Shu-Hong4, YANG Chun-Ming5, WANG Hui-Cai6, YANG [J]. Acta Agron Sin, 2018, 44(01): 43-52. |
[2] | WANG Rui-Yun,JI Xu,LU Ping,LIU Min-Xuan,XU Yue,WANG Lun,WANG Hai-Gang,QIAO Zhi-Jun. Analysis of Genetic Diversity in Common Millet (Panicum miliaceum) Using Fluorescent SSR in China [J]. Acta Agron Sin, 2017, 43(04): 530-548. |
[3] | HONG Xue-Juan, HOU Jin-Feng, DING Hui, LI Yong-Chun, GAI Jun-Yi, GENG Han. Comparison of Two Genetic Maps of Soybean constructed by RIL Populations Derived from Combinations of Peking×7605 under Two Ecological Sites [J]. Acta Agron Sin, 2012, 38(04): 614-623. |
[4] | ZHANG Yuan-Yuan, SHU Ai-Ping, ZHANG Li-Na, CAO Gui-Lan, HAN Long-Zhi. Analysis of Genetic Structure for Indica Rice Landraces from Different Provinces in China [J]. Acta Agron Sin, 2011, 37(12): 2173-2178. |
[5] | TUN Cheng-Lai, ZHANG Qian-Qian, DONG Bing-Xue, ZHANG Chun-Qing. Analysis of Genetic Structure and Genetic Relationships of Partial Maize Inbred Lines in China [J]. Acta Agron Sin, 2010, 36(11): 1820-1831. |
[6] | QIAO Ting-Ting,MA Chun-Lei,ZHOU Yan-Hua,YAO Ming-Zhe,LIU Rao,CHEN Liang. EST-SSR Genetic Diversity and Population Structure of Tea Landraces and Developed Cultivars (Lines) in Zhejiang Province, China [J]. Acta Agron Sin, 2010, 36(05): 744-753. |
[7] | QIN Jun,LI Ying-Hui,LIU Zhang-Xiong,LUAN Wei-Jiang,YAN Zhe,GUAN Rong-Xia,ZHANG Meng-Chen,CHANG Ru-Zhen,LI Guang-Min. Genetic Structure and Diversity of Soybean Germplasm in Heilongjiang in China [J]. Acta Agron Sin, 2009, 35(2): 228-238. |
[8] | ZHANG Jun;ZHAO Tuan-Jie;GAI Jun-Yi. Genetic Diversity and Genetic Structure of Soybean Cultivar Population Released in Northeast China [J]. Acta Agron Sin, 2008, 34(09): 1529-1536. |
|