Construction of Soybean Genetic Map Based on SLAF Markers and QTL Mapping Analysis of Salt Tolerance at Seedling Stage

doi:10.13560/j.cnki.biotech.bull.1985.2022-0579

Abstract

Abstract:

QTL mapping of salt tolerance traits in soybean seedling stage was carried out for two consecutive years to provide new gene loci for salt tolerance traits in soybean seedling stage, and to provide basis for in-depth understanding of genetic effects controlling salt tolerance and its location on chromosomes. The recombinant inbred line population（RIL）derived from the crossing of cultivated soybean variety Jinda 53 as female parent and wild soybean variety Pingnan as male parent was used as materials. At the seedling stage of soybean, the plant death concentration（PDC）was used as salt tolerance index after salt treatment, combined with the soybean genetic map constructed based on SLAF markers, the QTL loci of salt tolerance traits in soybean seedlings were detected by composite interval mapping method. The results showed that a total of 12 QTL loci were detected in different environments in two years, which were distributed on chromosome 2, 3, 5, 7, 9, 11, 13, 15, 18 and 20. The interpretation rate of genetic variation was 23.24%-38.28%. Among them, 2 QTL loci were distributed on chromosome 3, 2 QTL loci were distributed on chromosome 7, and the other 8 QTL loci were distributed in different chromosome segments. Among the 12 QTLs, 5 were consistent with the results of previous studies, and the remaining 7 QTL loci were new findings of salt tolerance in soybean seedlings.

Key words: soybean, seedling stage, salt tolerance, recombinant inbred line, QTL

CHEN Yi-bo, YANG Wan-ming, YUE Ai-qin, WANG Li-xiang, DU Wei-jun, WANG Min. Construction of Soybean Genetic Map Based on SLAF Markers and QTL Mapping Analysis of Salt Tolerance at Seedling Stage[J]. Biotechnology Bulletin, 2023, 39(2): 70-79.

Figures/Tables 9

References 38

[1]	Chen HT, Liu XQ, Zhang HM, et al. Advances in salinity tolerance of soybean: genetic diversity, heredity, and gene identification contribute to improving salinity tolerance[J]. J Integr Agric, 2018, 17(10): 2215-2221. doi: 10.1016/S2095-3119(17)61864-1 URL
[2]	胡一, 韩霁昌, 张扬. 盐碱地改良技术研究综述[J]. 陕西农业科学, 2015, 61(2): 67-71.
	Hu Y, Han JC, Zhang Y. Review of saline-alkali land improvement technology[J]. Shaanxi J Agric Sci, 2015, 61(2): 67-71.
[3]	李彬, 王志春, 孙志高, 等. 中国盐碱地资源与可持续利用研究[J]. 干旱地区农业研究, 2005, 23(2): 154-158.
	Li B, Wang ZC, Sun ZG, et al. Resources and sustainable resource exploitation of salinized land in China[J]. Agric Res Arid Areas, 2005, 23(2): 154-158.
[4]	刘梅芳, 樊琦. 中国大豆消费、生产和进口现状及存在的问题[J]. 粮食科技与经济, 2021, 46(6): 28-35.
	Liu MF, Fan Q. Study on the current situation and problems of soybean consumption, production and import in China[J]. Grain Sci Technol Econ, 2021, 46(6): 28-35.
[5]	Munns R, Tester M. Mechanisms of salinity tolerance[J]. Annu Rev Plant Biol, 2008, 59: 651-681. doi: 10.1146/annurev.arplant.59.032607.092911 pmid: 18444910
[6]	刘铎, 丛日春, 党宏忠, 等. 柳树幼苗渗透调节物质对中、碱性钠盐响应的差异性[J]. 生态环境学报, 2014, 23(9): 1531-1535.
	Liu D, Cong RC, Dang HZ, et al. Comparative effects of salt and alkali stresses on plant physiology of willow[J]. Ecol Environ Sci, 2014, 23(9): 1531-1535.
[7]	陈成升, 谢志霞, 刘小京. 渗盐分、干旱胁迫下冬小麦叶片部分渗透调节物质的动态变化[J]. 植物研究, 2009, 29(6): 708-713. doi: 10.7525/j.issn.1673-5102.2009.06.012
	Chen CS, Xie ZX, Liu XJ. Dynamic transformation of the substances of osmotic adjustment in winter wheat under iso-osmotic salt and drought stresses[J]. Bull Bot Res, 2009, 29(6): 708-713.
[8]	Zörb C, Geilfus CM, Dietz KJ. Salinity and crop yield[J]. Plant Biol(Stuttg), 2019, 21(Suppl 1): 31-38.
[9]	Zhu JK. Plant salt stress[J]. Encyclopedia of Life Sciences(eLS), 2007. DOI: 10.1002/9780470015902.a0001300.pub2. doi: 10.1002/9780470015902.a0001300.pub2
[10]	Xu DH, Tuyen DD. Genetic studies on saline and sodic tolerances in soybean[J]. Breed Sci, 2012, 61(5): 559-565. doi: 10.1270/jsbbs.61.559 URL
[11]	陈华涛, 陈新, 喻德跃, 等. 大豆耐盐基因定位及耐盐基因克隆研究进展[J]. 江苏农业科学, 2010, 38(5): 78-80.
	Chen HT, Chen X, Yu DY, et al. Research progress on localization and cloning of salt tolerance genes in soybean[J]. Jiangsu Agric Sci, 2010, 38(5): 78-80.
[12]	Guan RX, Qu Y, Guo Y, et al. Salinity tolerance in soybean is modulated by natural variation in GmSALT3[J]. Plant J, 2014, 80(6): 937-950. doi: 10.1111/tpj.12695 URL
[13]	Zhang W, Liao XL, Cui YM, et al. A cation diffusion facilitator, GmCDF1, negatively regulates salt tolerance in soybean[J]. PLoS Genet, 2019, 15(1): e1007798.
[14]	唐晓飞, 董兴月, 魏崃, 等. 转大豆Na⁺/H⁺逆向转运蛋白GmNHX1基因植株的获得[J]. 分子植物育种, 2016, 14(4): 904-909.
	Tang XF, Dong XY, Wei L, et al. Obtaining transgenic soybean plants with Na⁺/H⁺ antiporter(GmNHX1)[J]. Mol Plant Breed, 2016, 14(4): 904-909.
[15]	Sun TJ, Fan L, Yang J, et al. A Glycine max sodium/hydrogen exchanger enhances salt tolerance through maintaining higher Na⁺efflux rate and K⁺/Na⁺ ratio in Arabidopsis[J]. BMC Plant Biol, 2019, 19(1): 469. doi: 10.1186/s12870-019-2084-4 URL
[16]	Zhao XF, Wei PP, Liu Z, et al. Soybean Na⁺/H⁺ antiporter GmsSOS1 enhances antioxidant enzyme activity and reduces Na⁺ accumulation in Arabidopsis and yeast cells under salt stress[J]. Acta Physiol Plant, 2016, 39(1): 1-11. doi: 10.1007/s11738-016-2300-x URL
[17]	Wei PP, Wang LC, Liu AL, et al. GmCLC1 confers enhanced salt tolerance through regulating chloride accumulation in soybean[J]. Front Plant Sci, 2016, 7: 1082.
[18]	Chen HT, Chen X, Gu HP, et al. GmHKT1;4, a novel soybean gene regulating Na⁺/K⁺ ratio in roots enhances salt tolerance in transgenic plants[J]. Plant Growth Regul, 2014, 73(3): 299-308. doi: 10.1007/s10725-014-9890-3 URL
[19]	Liao Y, Zou HF, Wang HW, et al. Soybean GmMYB76, GmMYB92, and GmMYB177 genes confer stress tolerance in transgenic Arabidopsis plants[J]. Cell Res, 2008, 18(10): 1047-1060. doi: 10.1038/cr.2008.280 URL
[20]	Wang F, Chen HW, Li QT, et al. GmWRKY27 interacts with GmMYB174 to reduce expression of GmNAC29 for stress tolerance in soybean plants[J]. Plant J, 2015, 83(2): 224-236. doi: 10.1111/tpj.12879 URL
[21]	Liao Y, Zou HF, Wei W, et al. Soybean GmbZIP44, GmbZIP62 and GmbZIP78 genes function as negative regulator of ABA signaling and confer salt and freezing tolerance in transgenic Arabidopsis[J]. Planta, 2008, 228(2): 225-240. doi: 10.1007/s00425-008-0731-3 URL
[22]	Zhang GY, Chen M, Li LC, et al. Overexpression of the soybean GmERF3gene, an AP2/ERF type transcription factor for increased tolerances to salt, drought, and diseases in transgenic tobacco[J]. J Exp Bot, 2009, 60(13): 3781-3796. doi: 10.1093/jxb/erp214 URL
[23]	Pinheiro GL, Marques CS, Costa MDBL, et al. Complete inventory of soybean NAC transcription factors: sequence conservation and expression analysis uncover their distinct roles in stress response[J]. Gene, 2009, 444(1/2): 10-23. doi: 10.1016/j.gene.2009.05.012 URL
[24]	Sun XW, Liu DY, Zhang XF, et al. SLAF-seq: an efficient method of large-scale de novo SNP discovery and genotyping using high-throughput sequencing[J]. PLoS One, 2013, 8(3): e58700. doi: 10.1371/journal.pone.0058700 URL
[25]	Liu DY, Ma CX, Hong WG, et al. Construction and analysis of high-density linkage map using high-throughput sequencing data[J]. PLoS One, 2014, 9(6): e98855. doi: 10.1371/journal.pone.0098855 URL
[26]	王聪, 朱月林, 杨立飞, 等. 菜用大豆耐盐品种的筛选及其耐盐生理特性[J]. 江苏农业学报, 2009, 25(3): 621-627.
	Wang C, Zhu YL, Yang LF, et al. Screening of vegetable soybean cultivars for salt tolerance and their physiological characteristics[J]. Jiangsu J Agric Sci, 2009, 25(3): 621-627.
[27]	McCouch SR, Cho YG, Yano M, et al. Report on QTL nomenclature[J]. Rice Genet Newsl, 1997, 14: 11-13.
[28]	张威, 廖锡良, 喻德跃, 等. 大豆耐盐性研究进展[J]. 土壤与作物, 2018, 7(3): 284-292.
	Zhang W, Liao XL, Yu DY, et al. A review of salt tolerance in soybean(Glycine max(L.)Merill)[J]. Soils Crops, 2018, 7(3): 284-292.
[29]	Lee GJ, Carter TE, Villagarcia MR, et al. A major QTL conditioning salt tolerance in S-100 soybean and descendent cultivars[J]. TAG Theor Appl Genet Theor Und Angewandte Genet, 2004, 109(8): 1610-1619.
[30]	Hamwieh A, Tuyen DD, Cong H, et al. Identification and validation of a major QTL for salt tolerance in soybean[J]. Euphytica, 2011, 179(3): 451-459. doi: 10.1007/s10681-011-0347-8 URL
[31]	Chen HT, Cui SY, Fu SX, et al. Identification of quantitative trait loci associated with salt tolerance during seedling growth in soybean(Glycine max L.)[J]. Aust J Agric Res, 2008, 59(12): 1086. doi: 10.1071/AR08104 URL
[32]	Ha BK, Vuong TD, Velusamy V, et al. Genetic mapping of quantitative trait loci conditioning salt tolerance in wild soybean(Glycine soja)PI 483463[J]. Euphytica, 2013, 193(1): 79-88. doi: 10.1007/s10681-013-0944-9 URL
[33]	杨燕. 大豆幼苗期耐盐QTL的定位及候选基因的克隆[D]. 南京: 南京农业大学, 2013.
	Yang Y. Mapping QTL conferring salt tolerance at seedling stage and cloning of candidate genes in soybean[D]. Nanjing: Nanjing Agricultural University, 2013.
[34]	方义生, 曹东, 杨红丽, 等. 大豆耐盐相关基因研究进展[J]. 中国油料作物学报, 2020, 42(4): 512-526.
	Fang YS, Cao D, Yang HL, et al. Research progress of salt-tolerance genes in soybean[J]. Chin J Oil Crop Sci, 2020, 42(4): 512-526.
[35]	闫玮雯. 大豆耐盐QTL定位及耐盐相关基因克隆[D]. 秦皇岛: 河北科技师范学院, 2012.
	Yan WW. QTL mapping and related gene cloning for salt tolerance in soybean[D]. Qinhuangdao: Hebei Normal University of Science & Technology, 2012.
[36]	Kan GZ, Zhang W, Yang WM, et al. Association mapping of soybean seed germination under salt stress[J]. Mol Genet Genomics, 2015, 290(6): 2147-2162. doi: 10.1007/s00438-015-1066-y pmid: 26001372
[37]	Do TD, Vuong TD, Dunn D, et al. Mapping and confirmation of loci for salt tolerance in a novel soybean germplasm, Fiskeby III[J]. Theor Appl Genet, 2018, 131(3): 513-524. doi: 10.1007/s00122-017-3015-0 pmid: 29151146
[38]	刘谢香. 大豆苗期耐盐基因GmSALT3标记开发利用及出苗期耐盐QTL发掘[D]. 北京: 中国农业科学院, 2019.
	Liu XX. Marker development and utilization of salt tolerance gene GmSALT3 at seedling stage and QTL mapping for salt tolerance at emergence stage in soybean[D]. Beijing: Chinese Academy of Agricultural Sciences, 2019.

染色体 Chromosome	染色体长度 Chromosome length/cM	标记数 Number of markers	平均图距 Average distance/cM	最大Gap Max gap/cM	Gap长度<5 cM的比例 Proportion of those with gap<5 cM
1	152.35	57	2.67	16.24	0.88
2	208.45	577	0.36	9.13	1.00
3	121.27	68	1.78	9.17	0.94
4	132.43	528	0.25	9.45	0.99
5	164.72	499	0.33	3.34	1.00
6	163.35	404	0.40	9.44	1.00
7	208.22	366	0.57	7.31	0.98
8	176.81	580	0.30	9.87	0.99
9	146.00	414	0.35	17.92	0.99
10	144.33	608	0.24	23.12	1.00
11	119.15	105	1.13	8.12	0.97
12	149.87	545	0.27	25.26	1.00
13	138.98	274	0.51	15.38	0.98
14	174.33	120	1.45	16.63	0.96
15	149.64	616	0.24	8.19	1.00
16	92.51	28	3.30	16.15	0.85
17	193.28	214	0.90	6.87	0.99
18	196.48	740	0.27	27.09	0.99
19	106.30	534	0.20	9.76	0.99
20	209.99	668	0.31	28.45	0.98

染色体 Chromosome	染色体长度 Chromosome length/cM	标记数 Number of markers	平均图距 Average distance/cM	最大Gap Max gap/cM	Gap长度<5 cM的比例 Proportion of those with gap<5 cM
1	152.35	57	2.67	16.24	0.88
2	208.45	577	0.36	9.13	1.00
3	121.27	68	1.78	9.17	0.94
4	132.43	528	0.25	9.45	0.99
5	164.72	499	0.33	3.34	1.00
6	163.35	404	0.40	9.44	1.00
7	208.22	366	0.57	7.31	0.98
8	176.81	580	0.30	9.87	0.99
9	146.00	414	0.35	17.92	0.99
10	144.33	608	0.24	23.12	1.00
11	119.15	105	1.13	8.12	0.97
12	149.87	545	0.27	25.26	1.00
13	138.98	274	0.51	15.38	0.98
14	174.33	120	1.45	16.63	0.96
15	149.64	616	0.24	8.19	1.00
16	92.51	28	3.30	16.15	0.85
17	193.28	214	0.90	6.87	0.99
18	196.48	740	0.27	27.09	0.99
19	106.30	534	0.20	9.76	0.99
20	209.99	668	0.31	28.45	0.98

性状 Trait	亲本 Parents			重组自交群体 RIL
性状 Trait	晋大53 Jinda 53	平南Pingnan	显著性Significance	均值±标准差Mean±SD	变异系数CV/%	偏度Skewness	峰度Kurtosis
2021PDCⅠ	15	3	**	8.566 9±2.252 3	26.3	0.18	-0.521
2021PDC II	15	2	**	8.480 2±2.687 3	31.6	-0.089	-0.019
2021PDCⅢ	14	2	**	7.790 3±2.235 2	28.7	0.053	-0.105
2021PDCA	15	3	**	8.284 3±1.860 9	22.5	0.215	0.427
2020PDCⅠ	14	2	**	7.752 0±2.367 0	35.1	0.030	-0.825
2020PDC II	14	2	**	8.291 3±1.975 4	31.4	0.060	-0.762
2020PDCⅢ	14	4	**	7.610 2±1.518 2	22.9	0.211	-0.609
2020PDCA	14	3	**	7.883 5±1.445 4	22.1	0.264	-0.763

性状 Trait	亲本 Parents			重组自交群体 RIL
性状 Trait	晋大53 Jinda 53	平南Pingnan	显著性Significance	均值±标准差Mean±SD	变异系数CV/%	偏度Skewness	峰度Kurtosis
2021PDCⅠ	15	3	**	8.566 9±2.252 3	26.3	0.18	-0.521
2021PDC II	15	2	**	8.480 2±2.687 3	31.6	-0.089	-0.019
2021PDCⅢ	14	2	**	7.790 3±2.235 2	28.7	0.053	-0.105
2021PDCA	15	3	**	8.284 3±1.860 9	22.5	0.215	0.427
2020PDCⅠ	14	2	**	7.752 0±2.367 0	35.1	0.030	-0.825
2020PDC II	14	2	**	8.291 3±1.975 4	31.4	0.060	-0.762
2020PDCⅢ	14	4	**	7.610 2±1.518 2	22.9	0.211	-0.609
2020PDCA	14	3	**	7.883 5±1.445 4	22.1	0.264	-0.763

性状 Trait	2021PDCⅠ	2021PDC II	2021PDCⅢ	2021PDCA	2020PDCⅠ	2020PDC II	2020PDCⅢ	2020PDCA
2021PDCⅠ	1
2021PDC II	0.972 8**	1
2021PDCⅢ	0.821 9**	0.999 8**	1
2021PDCA	0.808 1**	0.999 7**	0.999 9**	1
2020PDCⅠ	0.651**	0.995 5**	0.999 9**	0.999 9**	1
2020PDC II	0.631 2**	0.601 4**	0.870 9**	0.881 8**	0.959 1**	1
2020PDCⅢ	0.591 7**	0.656 2**	0.664 5**	0.681 8**	0.832 1**	0.999 9**	1
2020PDCA	0.323 7**	0.362 9**	0.398 6**	0.415 5**	0.689 2**	0.995 4**	0.999 9**	1