野生大豆染色体片段代换系群体中与百粒重关联的野生片段及其候选基因

doi:10.3724/SP.J.1006.2022.14140

作物学报 ›› 2022, Vol. 48 ›› Issue (8): 1884-1893.doi: 10.3724/SP.J.1006.2022.14140

• 作物遗传育种·种质资源·分子遗传学 • 上一篇下一篇

野生大豆染色体片段代换系群体中与百粒重关联的野生片段及其候选基因

刘成(), 张雅轩, 陈先连, 韩伟, 邢光南, 贺建波, 张焦平, 张逢凯, 孙磊, 李宁, 王吴彬^*(), 盖钧镒^*()

南京农业大学大豆研究所 / 国家大豆改良中心 / 农业农村部大豆生物学与遗传育种重点实验室(综合) / 作物遗传与种质创新国家重点实验室 / 江苏省现代作物生产协同创新中心, 江苏南京 210095

收稿日期:2021-08-06 接受日期:2021-11-29 出版日期:2022-08-12 网络出版日期:2021-12-17
通讯作者: 王吴彬,盖钧镒
作者简介:E-mail: wildsoybean@163.com
基金资助:
江苏省农业科技自主创新资金项目(CX(20)2007);中央高校基本科研业务费专项(KYZ202103);国家自然科学基金项目(31601325);长江学者和创新团队发展计划项目(PCSIRT_17R55);国家现代农业产业技术体系建设专项(CARS-04)

Wild segments associated with 100-seed weight and their candidate genes in a wild chromosome segment substitution line population

LIU Cheng(), ZHANG Ya-Xuan, CHEN Xian-Lian, HAN Wei, XING Guang-Nan, HE Jian-Bo, ZHANG Jiao-Ping, ZHANG Feng-Kai, SUN Lei, LI Ning, WANG Wu-Bin^*(), GAI Jun-Yi^*()

Soybean Research Institute / National Center for Soybean Improvement / Key Laboratory for Biology and Genetic Improvement of Soybean (General) of Ministry of Agriculture and Rural Affairs / National Key Laboratory of Crop Genetics and Germplasm Enhancement / Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China

Received:2021-08-06 Accepted:2021-11-29 Published:2022-08-12 Published online:2021-12-17
Contact: WANG Wu-Bin,GAI Jun-Yi
Supported by:
Jiangsu Agriculture Science and Technology(CX(20)2007);Fundamental Research Funds for the Central Universities(KYZ202103);National Natural Science Foundation of China(31601325);MOE Program for Changjiang Scholars and Innovative Research Team in University(PCSIRT_17R55);China Agriculture Research System(CARS-04)

摘要/Abstract

摘要：

一年生野生大豆是栽培大豆的祖先, 在长期驯化改良过程中, 百粒重逐渐增大, 阐明该变化的遗传基础, 对大豆的进化研究与品种改良具有重要意义。为了解析大豆百粒重驯化的遗传基础, 本研究以177份全基因组重测序的野生大豆染色体片段代换系(SojaCSSLP5)为材料, 通过3个不同环境的表型评价, 检测到13个与大豆百粒重相关的野生染色体片段, 均具有减小大豆百粒重的加性效应, 变幅为-0.49~ -1.19 g, 这与野生大豆具有较小百粒重相符。检测到的这些野生染色体片段分布在大豆11条染色体上, 可以解释76.70%的表型变异, 单个片段表型贡献率变幅为2.45%~15.14%。其中片段Gm03_LDB_15和Gm12_LDB_46的贡献率超过10%, 为大豆百粒重由野生向栽培进化的大效应片段。结合双亲栽培大豆南农1138-2和野生大豆N24852的转录组数据和基因组数据, 在这些区段内共预测到13个百粒重候选基因, 涉及以下调控植物种子大小的途径: 泛素蛋白激酶调控途径、G蛋白信号途径、裂原活化蛋白激酶途径、植物激素途径、转录调控因子途径和HAIKU途径。与前人利用栽培大豆的研究结果相比, 本研究检测到13个大豆百粒重相关野生染色体片段中有4个片段是新检测到的, 表明有9个野生染色体片段可能为野生大豆传递给栽培大豆的共享片段, 而这4个新检测到的野生染色体片段相对应栽培片段可能为栽培大豆特有的进化片段。

关键词: 野生大豆, 染色体片段代换系, 百粒重, 数量性状位点

Abstract:

Annual wild soybean is the ancestor of cultivated soybean. The 100-seed weight gradually increases in the long-term domestication process. Clarifying the genetic basis of this change is of great significance to the evolutionary research and variety improvement of soybean. In order to analyze the genetic basis of 100-seed weight during soybean domestication, a wild soybean chromosome segment substitution line population (SojaCSSLP5) composed of 177 whole-genome resequencing lines were used in this study. 13 QTLs/segments of 100-seed weight were detected by phenotypic evaluation in three different environments. All of 13 wild chromosome segments had the additive effect of reducing 100-seed weight, ranging from -0.49 g to -1.19 g, which was consistent with the smaller 100-seed weight of wild soybeans. These detected domesticated segments from 11 chromosomes explained 76.70% of the phenotypic variation, and the phenotypic contribution rate of a single segment ranged from 2.45% to 15.14%. The contribution rate of segments Gm03_LDB_15 and Gm12_LDB_46 exceeded 10%, which were major influence on the evolution of 100-seed weight of wild soybeans. Combined the transcriptome data and genome data of parental cultivated soybean Nannong 1138-2 and wild soybean N24852, a total of 13 candidate genes were predicted in these segments, and were involved in the pathways of plant seed size, including ubiquitin protein kinase regulatory pathway, G protein signal pathway, mitogen-activated protein kinase pathway, plant hormone pathway, transcription regulator pathway, and IKU (HAIKU) pathway. Compared with previous QTLs mapping results with cultivated soybeans, 4 of the 13 QTLs/segments were newly detected in this study, indicating that 9 wild chromosome segments might be passed to cultivated soybeans during domestication, and the corresponding cultivated segments of these 4 wild segments may be unique evolutionary segments of cultivated soybean.

Key words: wild soybean, chromosome segment substitution line, 100-seed weight, QTLs

刘成, 张雅轩, 陈先连, 韩伟, 邢光南, 贺建波, 张焦平, 张逢凯, 孙磊, 李宁, 王吴彬, 盖钧镒. 野生大豆染色体片段代换系群体中与百粒重关联的野生片段及其候选基因[J]. 作物学报, 2022, 48(8): 1884-1893.

LIU Cheng, ZHANG Ya-Xuan, CHEN Xian-Lian, HAN Wei, XING Guang-Nan, HE Jian-Bo, ZHANG Jiao-Ping, ZHANG Feng-Kai, SUN Lei, LI Ning, WANG Wu-Bin, GAI Jun-Yi. Wild segments associated with 100-seed weight and their candidate genes in a wild chromosome segment substitution line population[J]. Acta Agronomica Sinica, 2022, 48(8): 1884-1893.

图/表 5

表1

表2

表3

图1

表4

结合南农1138-2和N24852转录组及基因组数据预测的大豆百粒重候选基因"

基因 Gene	片段 QTL	基因功能 Function	亲本 Parents	变异碱基 SNP variant	差异表达 Expression difference (FPKM)
基因 Gene	片段 QTL	基因功能 Function	亲本 Parents	变异碱基 SNP variant	14 seed	21 seed	28 seed	35 seed	Leaf
Glyma.02G125200	qSW2.1	bHLH转录因子^[39] bHLH transcription factor^[39]	南农1138-2 Nannong 1138-2	TCGG	0.45	0.40	2.19	5.37	2.57
		bHLH转录因子^[39] bHLH transcription factor^[39]	N24852	CAAT	13.79	6.11	8.71	21.03	91.63
Glyma.03G066200	qSW3.1	ABA受体调节因子(IKU) Regulatory components of ABA receptor (IKU)	南农1138-2 Nannong 1138-2	GA	1.25	0.63	3.91	10.63	0.69
		ABA受体调节因子(IKU) Regulatory components of ABA receptor (IKU)	N24852	AG	3.16	1.39	3.48	20.33	2.93
Glyma.04G080800	qSW4.1	RNA聚合酶I相关因子 RNA polymerase I-associated factor	南农1138-2 Nannong 1138-2	G	48.56	53.32	13.06	16.68	16.63
		RNA聚合酶I相关因子 RNA polymerase I-associated factor	N24852	C	39.16	18.85	35.88	108.75	14.82
Glyma.04G078900	qSW4.2	裂原活化蛋白激酶 Mitogen-activated protein kinase	南农1138-2 Nannong 1138-2	G	0.80	0.42	2.21	2.27	0.93
		裂原活化蛋白激酶 Mitogen-activated protein kinase	N24852	C	11.43	5.44	5.54	9.74	7.88
Glyma.04G116700	qSW4.3	对生长素的反应 Response to auxin	南农1138-2 Nannong 1138-2	AACACGC	1.11	0.71	3.82	7.24	1.01
		对生长素的反应 Response to auxin	N24852	CGTCGAT	10.27	5.20	17.85	45.44	10.32
Glyma.06G146700	qSW6.1	调节发育的G蛋白^[40] G protein that regulates development^[40]	南农1138-2 Nannong 1138-2	TTCTTTC	0.41	0.68	2.28	4.90	0.77
		调节发育的G蛋白^[40] G protein that regulates development^[40]	N24852	CCTACCA	11.03	11.03	17.77	41.99	11.34
Glyma.09G194200	qSW9.1	丝氨酸/苏氨酸磷酸酶 Serine/threonine phosphatase	南农1138-2 Nannong 1138-2	CCCCTTCTCT	1.44	0.39	0.80	0.50	1.26
		丝氨酸/苏氨酸磷酸酶 Serine/threonine phosphatase	N24852	TTATCATAGC	19.75	6.88	9.99	4.78	11.35
基因 Gene	片段 QTL	基因功能 Function	亲本 Parents	变异碱基 SNP variant	差异表达 Expression difference (FPKM)
基因 Gene	片段 QTL	基因功能 Function	亲本 Parents	变异碱基 SNP variant	14 seed	21 seed	28 seed	35 seed	Leaf
Glyma.11G063500	qSW11.1	E3泛素连接酶^[41⇓-43] E3 ubiquitin ligase^[41⇓-43]	南农1138-2 Nannong 1138-2	C	0.31	1.42	1.93	3.45	0.78
		E3泛素连接酶^[41⇓-43] E3 ubiquitin ligase^[41⇓-43]	N24852	G	6.33	8.77	6.09	17.65	7.58
Glyma.12G216100	qSW12.1	GRAS类转录因子 GRAS transcription factors	南农1138-2 Nannong 1138-2	TCG	1.49	1.84	12.80	30.95	1.17
		GRAS类转录因子 GRAS transcription factors	N24852	GGA	1.61	2.14	20.70	73.39	1.99
Glyma.13G167900	qSW13.1	核糖体生物合成蛋白 Ribosomal biosynthetic protein	南农1138-2 Nannong 1138-2	AGG	28.37	39.78	17.86	19.92	22.40
		核糖体生物合成蛋白 Ribosomal biosynthetic protein	N24852	GAA	33.04	12.85	39.50	104.52	15.60
Glyma.16G084300	qSW16.1	生长素响应因子 Auxin response factor	南农1138-2 Nannong 1138-2	G	0.31	0.46	0.88	0.11	3.24
		生长素响应因子 Auxin response factor	N24852	C	30.59	10.86	3.63	0.44	39.27
Glyma.18G200100	qSW18.1	E3泛素连接酶 E3 ubiquitin ligase	南农1138-2 Nannong 1138-2	GTATTAC	0.59	1.41	1.15	0.92	1.45
		E3泛素连接酶 E3 ubiquitin ligase	N24852	ACCCCGT	2.80	3.46	5.14	2.68	4.40
Glyma.19G004200	qSW19.1	亲环蛋白 Cyclophilin	南农1138-2 Nannong 1138-2	TGCACG	14.24	9.18	8.69	5.45	4.90
			N24852	AAAGTT	8.19	5.47	17.04	34.60	7.26

表4

参考文献 51

[1]	Zhou Z K, Jiang Y, Wang Z, Gou Z H, Lyu J, Li W Y, Yu Y J, Shu L P, Zhao Y J, Ma Y M, Fang C, Shen Y T, Liu T F, Li C C, Li Q, Wu M, Wang M, Wu Y S, Dong Y, Wan W T, Wang X, Ding Z L, Gao Y D, Xiang H, Zhu B G, Lee S H, Wang W, Tian Z X. Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean. Nat Biotechnol, 2015, 33: 408-416. doi: 10.1038/nbt.3096
[2]	Wang M, Li W Z, Fang C, Xu F, Liu Y C, Wang Z, Yang R, Zhang M, Liu S L, Lu S J, Lin T, Tang J Y, Wang Y Q, Wang H R, Lin H, Zhu B G, Chen M S, Kong F J, Liu B H, Zeng D L, Jackson S A, Chu C C, Tian Z X. Parallel selection on a dormancy gene during domestication of crops from multiple families. Nat Genet, 2018, 50: 1435-1441. doi: 10.1038/s41588-018-0229-2 pmid: 30250128
[3]	Liu B H, Watanabe S, Uchiyama T, Kong F J, Kanazawa A, Xia Z J, Nagamatsu A, Arai M, Yamada T, Kitamura K, Masuta C, Harada K, Abe J. The soybean stem growth habit gene Dt1is an ortholog of Arabidopsis TERMINAL FLOWER1. Plant Physiol, 2010, 153: 198-210. doi: 10.1104/pp.109.150607
[4]	Sun L, Miao Z, Cai C, Zhang D, Zhao M, Wu Y, Zhang X, Swarm S A, Zhou L, Zhang Z J, Nelson R L, Ma J. GmHs1-1, encoding a calcineurin-like protein, controls hard-seededness in soybean. Nat Genet, 2015, 47: 939-943. doi: 10.1038/ng.3339
[5]	Han Y P, Li D M, Zhu D, Li H Y, Li X P, Teng W L, Li W B. QTL analysis of soybean seed weight across multi-genetic backgrounds and environments. Theor Appl Genet, 2012, 125: 671-683. doi: 10.1007/s00122-012-1859-x
[6]	Kato S, Sayama T, Fujii K, Yumoto S, Kono Y, Hwang T Y, Kikuchi A, Takada Y, Tanaka Y, Shiraiwa T, Ishimoto M. A major and stable QTL associated with seed weight in soybean across multiple environments and genetic backgrounds. Theor Appl Genet, 2014, 127: 1365-1374. doi: 10.1007/s00122-014-2304-0
[7]	Xin D W, Qi Z M, Jiang H W, Hu Z B, Zhu R S, Hu J H, Han H Y, Hu G H, Liu C Y, Chen Q S. QTL location and epistatic effect analysis of 100-seed weight using wild soybean (Glycine soja Sieb. & Zucc.) chromosome segment substitution lines. PLoS One, 2016, 11: e0149380. doi: 10.1371/journal.pone.0149380
[8]	Liu D Q, Yan Y L, Fujita Y, Xu D H. Identification and validation of QTLs for 100-seed weight using chromosome segment substitution lines in soybean. Breed Sci, 2018, 68: 442-448. doi: 10.1270/jsbbs.17127
[9]	Wu D P, Zhan Y H, Sun Q X, Xu L X, Lian M, Zhao X, Han Y P, Li W B. Identification of quantitative trait loci underlying soybean (Glycine max [L.] Merr.) seed weight including main, epistatic and QTL × environment effects in different regions of Northeast China. Plant Breed, 2018, 137: 194-202. doi: 10.1111/pbr.12574
[10]	Li Y H, Reif J C, Hong H L, Li H H, Liu Z X, Ma Y S, Li J, Tian Y, Li Y F, Li W B, Qiu L J. Genome-wide association mapping of QTL underlying seed oil and protein contents of a diverse panel of soybean accessions. Plant Sci, 2018, 266: 95-101. doi: 10.1016/j.plantsci.2017.04.013
[11]	Li D M, Zhao X, Han Y P, Li W B, Xie F T. Genome-wide association mapping for seed protein and oil contents using a large panel of soybean accessions. Genomics, 2019, 111: 90-95. doi: 10.1016/j.ygeno.2018.01.004
[12]	Zhang Y H, He J B, Wang Y F, Xing G N, Zhao J M, Li Y, Yang S P, Palmer R G, Zhao T J, Gai J Y. Establishment of a 100-seed weight quantitative trait locus-allele matrix of the germplasm population for optimal recombination design in soybean breeding programmes. J Exp Bot, 2015, 66: 6311-6325. doi: 10.1093/jxb/erv342
[13]	He J B, Meng S, Zhao T J, Xing G N, Yang S P, Li Y, Guan R Z, Lu J J, Wang Y F, Xia Q J, Yang B, Gai J Y. An innovative procedure of genome-wide association analysis fits studies on germplasm population and plant breeding. Theor Appl Genet, 2017, 130: 2327-2343. doi: 10.1007/s00122-017-2962-9
[14]	Li D D, Pfeiffer T W, Cornelius P L. Soybean QTL for yield and yield components associated with Glycine soja alleles. Crop Sci, 2008, 48: 571-581. doi: 10.2135/cropsci2007.06.0361
[15]	Liu B, Fujita T, Yan Z H, Sakamoto S, Xu D, Abe J. QTL mapping of domestication-related traits in soybean (Glycine max). Ann Bot, 2007, 100: 1027-1038. doi: 10.1093/aob/mcm149
[16]	Maughan P J, Maroof M A S, Buss G R. Molecular-marker analysis of seed weight: genomic locations, gene action, and evidence for orthologous evolution among three legume species. Theor Appl Genet, 1996, 93: 574-579. doi: 10.1007/BF00417950 pmid: 24162350
[17]	Sebolt A M, Shoemaker R C, Diers B W. Analysis of a quantitative trait locus allele from wild soybean that increases seed protein concentration in soybean. Crop Sci, 2000, 40: 1438-1444. doi: 10.2135/cropsci2000.4051438x
[18]	Wang W B, He Q Y, Yang H Y, Xiang S H, Xing G N, Zhao T J, Gai J Y. Identification of QTL/segments related to seed-quality traits in G. soja using chromosome segment substitution lines. Plant Genet Resour, 2014, 12: S65-S69.
[19]	Yang K, Moon J K, Jeong N, Chun H K, Kang S T, Back K, Jeong S C. Novel major quantitative trait loci regulating the content of isoflavone in soybean seeds. Genes Genom, 2011, 33: 685-692. doi: 10.1007/s13258-011-0043-z
[20]	Wang W B, He Q Y, Yang H Y, Xiang S H, Zhao T J, Gai J Y. Development of a chromosome segment substitution line population with wild soybean (Glycine soja Sieb. et Zucc.) as donor parent. Euphytica, 2013, 189: 293-307. doi: 10.1007/s10681-012-0817-7
[21]	Chen Z L, Wang B B, Dong X M, Liu H, Ren L H, Chen J, Hauck A, Song W B, Lai J S. An ultra-high density bin-map for rapid QTL mapping for tassel and ear architecture in a large F₂ maize population. BMC Genomics, 2014, 15: 433. doi: 10.1186/1471-2164-15-433
[22]	Li G Q, Wang Y, Chen M S, Edae E, Poland J, Akhunov E, Chao S M, Bai G H, Carver B F, Yan L L. Precisely mapping a major gene conferring resistance to Hessian fly in bread wheat using genotyping-by-sequencing. BMC Genomics, 2015, 16: 108. doi: 10.1186/s12864-015-1297-7
[23]	Wu X L, Ren C W, Joshi T, Vuong T, Xu D, Nguyen H T. SNP discovery by high-throughput sequencing in soybean. BMC Genomics, 2010, 11: 469. doi: 10.1186/1471-2164-11-469
[24]	Xu X Y, Zeng L, Tao Y, Vuong T, Wan J R, Boerma R, Noe J, Li Z L, Finnerty S, Pathan S M, Shannon J G, Nguyen H T. Pinpointing genes underlying the quantitative trait loci for root-knot nematode resistance in palaeopolyploid soybean by whole genome resequencing. Proc Natl Acad Sci USA, 2013, 110: 13469-13474. doi: 10.1073/pnas.1222368110
[25]	Liu C, Chen X L, Wang W B, Hu X Y, Han W, He Q Y, Yang H Y, Xiang S H, Gai J Y. Identifying wild versus cultivated gene-alleles conferring seed coat color and days to flowering in soybean. Int J Mol Sci, 2021, 22: 1559-1580. doi: 10.3390/ijms22041559
[26]	Li Y H, Zheng L Y, Corke F, Smith C, Bevan M W. Control of final seed and organ size by the DA1 gene family in Arabidopsis thaliana Gene Dev, 2008, 22: 1331-1336. doi: 10.1101/gad.463608
[27]	Ashikari M, Wu J Z, Yano M, Sasaki T, Yoshimura A. Rice gibberellin-insensitive dwarf mutant gene Dwarf 1 encodes the α-subunit of GTP-binding protein. Proc Natl Acad Sci USA, 1999, 96: 10284-10289. doi: 10.1073/pnas.96.18.10284
[28]	Schruff M C, Spielman M, Tiwari S, Adams S, Fenby N, Scott R J. The AUXIN RESPONSE FACTOR 2 gene of Arabidopsis links auxin signalling, cell division, and the size of seeds and other organs. Development, 2006, 133: 251-261. pmid: 16339187
[29]	Garcia D, Saingery V, Chambrier P, Mayer U, Jurgens G, Berger F. Arabidopsis haiku mutants reveal new controls of seed size by endosperm. Plant Physiol, 2003, 131: 1661-1670. doi: 10.1104/pp.102.018762
[30]	Ishimaru K, Hirotsu N, Madoka Y, Murakami N, Hara N, Onodera H, Kashiwagi T, Ujiie K, Shimizu B, Onishi A, Miyagawa H, Katoh E. Loss of function of the IAA-glucose hydrolase gene TGW6 enhances rice grain weight and increases yield. Nat Genet, 2013, 45: 707-711. doi: 10.1038/ng.2612 pmid: 23583977
[31]	Meng L, Li H H, Zhang L Y, Wang J K. QTL IciMapping: integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations. Crop J, 2015, 3: 269-283. doi: 10.1016/j.cj.2015.01.001
[32]	Teng W, Han Y, Du Y, Sun D, Zhang Z, Qiu L, Sun G, Li W. QTL analyses of seed weight during the development of soybean (Glycine max L. Merr.). Heredity, 2009, 102: 372-380. doi: 10.1038/hdy.2008.108 pmid: 18971958
[33]	Vieira A J D, Oliveira D A D, Soares T C B, Schuster L, Piovesan N D, Martinez C A, Barros E G, Moreira M A. Use of the QTL approach to the study of soybean trait relationships in two populations of recombinant inbred lines at the F₇ and F₈ generations. Braz J Plant Physiol, 2006, 18: 281-290. doi: 10.1590/S1677-04202006000200004
[34]	Hacisalihoglu G, Burton A L, Gustin J L, Eker S, Asikli S, Heybet E H, Ozturk L, Cakmak I, Yazici A, Burkey K O, Orf J, Settles A M. Quantitative trait loci associated with soybean seed weight and composition under different phosphorus levels. J Integr Plant Biol, 2018, 60: 232-241. doi: 10.1111/jipb.12612
[35]	Sun Y N, Pan J B, Shi X L, Du X Y, Wu Q, Qi Z M, Jiang H W, Xin D W, Liu C Y, Hu G H, Chen Q S. Multi-environment mapping and meta-analysis of 100-seed weight in soybean. Mol Biol Rep, 2012, 39: 9435-9443. doi: 10.1007/s11033-012-1808-4
[36]	Funatsuki H, Kawaguchi K, Matsuba S, Sato Y, Ishimoto M. Mapping of QTL associated with chilling tolerance during reproductive growth in soybean. Theor Appl Genet, 2005, 111: 851-861. pmid: 16059730
[37]	Hyten D L, Pantalone V R, Sams C E, Saxton A M, Landau-Ellis D, Stefaniak T R, Schmidt M E. Seed quality QTL in a prominent soybean population. Theor Appl Genet, 2004, 109: 552-561. pmid: 15221142
[38]	Mian M A R, Bailey M A, Tamulonis J P, Shipe E R, Carter T E, Parrott W A, Ashley D A, Hussey R S, Boerma H R. Molecular markers associated with seed weight in two soybean populations. Theor Appl Genet, 1996, 93: 1011-1016. doi: 10.1007/BF00230118 pmid: 24162474
[39]	Luo J H, Liu H, Zhou T Y, Gu B G, Huang X H, Shang-Guan Y Y, Zhu J J, Li Y, Zhao Y, Wang Y C, Zhao Q, Wang A H, Wang Z Q, Sang T, Wang Z X, Han B. An-1 encodes a basic helix-loop-helix protein that regulates awn development, grain size, and grain number in rice. Plant Cell, 2013, 25: 3360-3376. doi: 10.1105/tpc.113.113589
[40]	Sun S Y, Wang L, Mao H L, Shao L, Li X H, Xiao J H, Ou-Yang Y D, Zhang Q F. A G-protein pathway determines grain size in rice. Nat Commun, 2018, 9: 851. doi: 10.1038/s41467-018-03141-y
[41]	Song X J, Huang W, Shi M, Zhu M Z, Lin H X. A QTL for rice grain width and weight encodes a previously unknown RING- type E3 ubiquitin ligase. Nat Genet, 2007, 39: 623-630. doi: 10.1038/ng2014
[42]	Dong H, Dumenil J, Lu F H, Na L, Vanhaeren H, Naumann C, Klecker M, Prior R, Smith C, McKenzie N, Saalbach G, Chen L L, Xia T, Gonzalez N, Seguela M, Inze D, Dissmeyer N, Li Y H, Bevan M W. Ubiquitylation activates a peptidase that promotes cleavage and destabilization of its activating E3 ligases and diverse growth regulatory proteins to limit cell proliferation in Arabidopsis. Gene Dev, 2017, 31: 197-208. doi: 10.1101/gad.292235.116 pmid: 28167503
[43]	Su Z Q, Hao C Y, Wang L F, Dong Y C, Zhang X Y. Identification and development of a functional marker of TaGW2 associated with grain weight in bread wheat (Triticum aestivum L.). Theor Appl Genet, 2011, 122: 211-223. doi: 10.1007/s00122-010-1437-z
[44]	Zhao B, Dai A, Wei H, Wang B, Jiang N, Feng X. Arabidopsis KLU homologue GmCYP78A72 regulates seed size in soybean. Plant Mol Biol, 2016, 90: 33-47. doi: 10.1007/s11103-015-0392-0
[45]	Tang X F, Su T, Han M, Wei L, Wang W W, Yu Z Y, Xue Y G, Wei H B, Du Y J, Greiner S, Rausch T, Liu L J. Suppression of extracellular invertase inhibitor gene expression improves seed weight in soybean (Glycine max). J Exp Bot, 2017, 68: 469-482.
[46]	Ge L F, Yu J B, Wang H L, Luth D, Bai G H, Wang K, Chen R J. Increasing seed size and quality by manipulating BIG SEEDS1 in legume species. Proc Natl Acad Sci USA, 2016, 113: 12414-12419. doi: 10.1073/pnas.1611763113
[47]	Liu J Y, Zhang Y W, Han X, Zuo J F, Zhang Z, Shang H, Song Q, Zhang Y M. An evolutionary population structure model reveals pleiotropic effects of GmPDAT for traits related to seed size and oil content in soybean. J Exp Bot, 2020, 71: 6988-7002. doi: 10.1093/jxb/eraa426
[48]	Wang S D, Liu S, Wang J, Yokosho K, Zhou B, Yu Y C, Liu Z, Frommer W B, Ma J F, Chen L Q, Guan Y F, Shou H X, Tian Z X. Simultaneous changes in seed size, oil content, and protein content driven by selection of SWEET homologues during soybean domestication. Nat Sci Rev, 2020, 7: 1776-1786. doi: 10.1093/nsr/nwaa110
[49]	Lu X, Li Q T, Xiong Q, Li W, Bi Y D, Lai X L, Man W Q, Zhang W K, Ma B, Chen S Y, Zhang J S. The transcriptomic signature of developing soybean seeds reveals the genetic basis of seed trait adaptation during domestication. Plant J, 2016, 86: 530-544. doi: 10.1111/tpj.13181
[50]	Lu X, Xiong Q, Cheng T, Li Q T, Liu X L, Bi Y D, Li W, Zhang W K, Ma B, Lai Y C, Du W G, Man W Q, Chen S Y, Zhang J S. A PP2C-1 allele underlying a quantitative trait locus enhances soybean 100-seed weight. Mol Plant, 2017, 10: 670-684. doi: 10.1016/j.molp.2017.03.006
[51]	Nguyen C X, Paddock K J, Zhang Z Y, Stacey M G. GmKIX8-1 regulates organ size in soybean and is the causative gene for the major seed weight QTL qSw17-1. New Phytol, 2021, 229: 920-934. doi: 10.1111/nph.16928

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变异来源 Source of variation	自由度 DF	均方 MS	F值 F-value	P
环境 Environment	2	417.90	398.00	<0.0001
环境内重复 Repeat (Environment)	6	8.03	7.65	<0.0001
家系 Line	176	29.31	12.06	<0.0001
家系×环境Line×Environment	356	2.43	2.31	<0.0001
误差 Error	1007	1.05
总和 Total	1549

QTL	连锁标记 Marker	染色体区间 Genome region	区间大小 Size of region (Mb)	显著性 LOD	贡献率 PVE (%)	加性效应 Add	已报道QTL Reported QTL
qSW2.1	Gm02_LDB_27	12586195-13747176	1.16	9.11	6.97	-0.77	Seed weight 49-8^[32]
qSW3.1	Gm03_LDB_15	12466486-13017335	0.55	17.63	15.14	-1.19	新位点New
qSW4.1	Gm04_LDB_13	2601664-2650056	0.05	5.62	4.10	-0.62	Seed weight 47-3^[33]
qSW4.2	Gm04_LDB_25	6482923-6818956	0.34	6.22	4.58	-0.58	Seed weight 54-1^[34] Seed weight 47-3^[33]
qSW4.3	Gm04_LDB_39	12291313-15488343	3.20	4.30	3.09	-0.57	Seed weight 50-9^[6] Seed weight 47-3^[33]
qSW6.1	Gm06_LDB_34	11933129-12135714	0.20	5.11	3.71	-0.49	新位点New
qSW9.1	Gm09_LDB_54	41753666-41795135	0.04	9.10	6.96	-0.59	Seed weight 27-3^[33]
qSW11.1	Gm11_LDB_21	4680921-4726090	0.05	8.95	6.83	-0.77	Seed weight 37-9^[35]
qSW12.1	Gm12_LDB_46	37389148-37916269	0.53	12.59	10.10	-1.08	新位点New
qSW13.1	Gm13_LDB_27	28160461-28502188	0.34	6.96	5.17	-0.67	Seed weight 50-7^[6] Seed weight 19-2^[36] Seed weight 15-3^[37] Seed weight 49-14^[32] Seed weight 2-4^[38]
qSW16.1	Gm16_LDB_38	8724531-9795523	1.07	5.31	3.86	-0.67	新位点New
qSW18.1	Gm18_LDB_24	43990050-47921961	3.93	3.45	2.45	-0.50	Seed weight 27-1^[33]
qSW19.1	Gm19_LDB_3	223110-353922	0.13	5.16	3.74	-0.49	Seed weight 3-6^[33]

野生大豆染色体片段代换系群体中与百粒重关联的野生片段及其候选基因

Wild segments associated with 100-seed weight and their candidate genes in a wild chromosome segment substitution line population

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环境 Environment	亲本 Parents		染色体片段代换系群体 Chromosome segment substitution line population (SojaCSSLP5)
	南农1138-2 Nannong 1138-2	N24852	组中值Class mid-value (g)													变幅 Range	均值 Mean	变异系数 CV (%)	遗传率 h² (%)
	南农1138-2 Nannong 1138-2	N24852				10	11	12	13	14	15	16	17	18	19	变幅 Range	均值 Mean	变异系数 CV (%)	遗传率 h² (%)	20	21	Σ
2016JP	18.07	1.84	1	3	4	9	30	43	47	31	7	2	0	0	177	10.49-18.85	15.34	6.45	84.2
2017JP	19.22	1.79	2	2	4	8	21	30	40	36	24	8	1	1	177	10.00-21.18	15.91	6.52	89.0
2018DT	19.56	1.74	0	0	2	2	12	16	26	36	40	34	8	1	177	12.10-20.78	17.14	6.08	86.6
平均Mean	18.95	1.73	0	1	3	6	12	28	46	54	23	4	0	0	177	11.15-18.96	16.14	6.36	91.8

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