基于Super-GBS的高粱株高和节间数QTL定位

doi:10.13560/j.cnki.biotech.bull.1985.2022-1510

摘要/Abstract

摘要：

株高及相关性状是影响高粱株型和产量的关键因素，定位影响这些性状的主效QTL，为高粱的分子遗传改良提供依据。以美国高粱品种BTx623和贵州酒用高粱品种红缨子杂交构建的包含205个家系的重组自交系（RIL）群体为材料，在5个环境条件下调查株高和节间数。利用Super-GBS技术进行基因分型，建立SNP标记遗传图谱，采用完备区间作图法（ICIM）开展QTL定位。结果表明，在第1、3、4、8、9染色体上一共检测到18个QTL，其中，与株高和节间数相关的QTL分别为7和11个。有10个主效QTL在多个环境中或2个性状中被重复检测到，其中qPH9.1与已知的株高基因Dw1一致，而qPH1.2、qPH3.2、qIN3.2以及qIN8.1所在区间内包含了4个与影响水稻株高或节间伸长的基因同源。

关键词: 高粱, 株高, 节间数, QTL定位, 候选基因

Abstract:

Plant height and its relative traits are key factors that affect plant type and yield of sorghum. Mapping major QTL for these traits may provide a basis for genetic improvement in sorghum. In this study, a RI population including 205 lines obtained from a cross between American cultivar BTx623 and Guizhou liquor-brewing cultivar Hongyingzi was used to investigate plant height and internode numbers under five environments. The genetic map was constructed based on genotype data from Super-GBS technology, and major QTLs were identified by inclusive composite interval mapping（ICIM）. Totally, eighteen major QTLs were detected on chromosome 1, 3, 4, 8, and 9, of which 7 and 11 QTLs were related to plant height and internode numbers, respectively. Ten major QTLs were repeatedly detected in multiple environments or two traits, of which qPH9.1 was consistent with the known plant high gene Dw1, while qPH1.2, qPH3.2, qIN3.2 and qIN8.1 were colocalized with four homologous genes involving in plant height or internode elongation in rice.

Key words: sorghum, plant height, number of internodes, QTL mapping, candidate genes

徐建霞, 丁延庆, 冯周, 曹宁, 程斌, 高旭, 邹桂花, 张立异. 基于Super-GBS的高粱株高和节间数QTL定位[J]. 生物技术通报, 2023, 39(7): 185-194.

XU Jian-xia, DING Yan-qing, FENG Zhou, CAO Ning, CHENG Bin, GAO Xu, ZOU Gui-hua, ZHANG Li-yi. QTL Mapping of Sorghum Plant Height and Internode Numbers Based on Super-GBS Technique[J]. Biotechnology Bulletin, 2023, 39(7): 185-194.

图/表 7

参考文献 42

[1]	李顺国, 刘猛, 刘斐, 等. 中国高粱产业和种业发展现状与未来展望[J]. 中国农业科学, 2021, 54(3): 471-482. doi: 10.3864/j.issn.0578-1752.2021.03.002
	Li SG, Liu M, Liu F, et al. Current status and future prospective of sorghum production and seed industry in China[J]. Sci Agric Sin, 2021, 54(3): 471-482. doi: 10.3864/j.issn.0578-1752.2021.03.002
[2]	仪治本, 梁小红, 赵威军, 等. 高粱基因组遗传图谱构建的研究进展[J]. 农业生物技术学报, 2006, 14(2): 279-285.
	Yi ZB, Liang XH, Zhao WJ, et al. Advances in genetic mapping of sorghum genome[J]. J Agric Biotechnol, 2006, 14(2): 279-285.
[3]	高士杰, 刘晓辉, 李继洪. 高粱高产育种应重视株型和穗结构性状的改良[J]. 种子, 2007, 26(3): 83-84.
	Gao SJ, Liu XH, Li JH. Paying much attention to the improvement of plant type and spike structure in high-yielding breeding of sorghum[J]. Seed, 2007, 26(3): 83-84.
[4]	Baggett JP, Tillett RL, Cooper EA, et al. De novo identification and targeted sequencing of SSRs efficiently fingerprints sorghum bicolor sub-population identity[J]. PLoS One, 2021, 16(3): e0248213.
[5]	Wang LM, Jiao SJ, Jiang YX, et al. Genetic diversity in parent lines of sweet sorghum based on agronomical traits and SSR markers[J]. Field Crops Res, 2013, 149: 11-19. doi: 10.1016/j.fcr.2013.04.013 URL
[6]	Reddy RN, Madhusudhana R, Mohan SM, et al. Mapping QTL for grain yield and other agronomic traits in post-rainy sorghum[Sor-ghum bicolor(L.) Moench[J]. Theor Appl Genet, 2013, 126(8): 1921-1939. doi: 10.1007/s00122-013-2107-8 URL
[7]	苏舒. 高粱形态学农艺性状的QTL定位研究[D]. 南京: 南京大学, 2012.
	Su S. QTL mapping of agronomic traits of morphology in sorghum[D]. Nanjing: Nanjing University, 2012.
[21]	Ding YQ, Xu JX, Wang C, et al. QTL mapping of grain traits related to brewing in sorghum based on super-GBS technology[J]. J Nucl Agric Sci, 2023, 37(2): 241-250. doi: 10.11869/j.issn.1000-8551.2023.02.0241
[22]	Meng L, Li HH, Zhang LY, et al. QTL IciMapping: integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations[J]. Crop J, 2015, 3(3): 269-283. doi: 10.1016/j.cj.2015.01.001
[23]	丁延庆, 周棱波, 汪灿, 等. 酱香型酒用糯高粱研究进展[J]. 生物技术通报, 2019, 35(5): 28-34. doi: 10.13560/j.cnki.biotech.bull.1985.2019-0080 URL
	Ding YQ, Zhou LB, Wang C, et al. Research advance in glutinous sorghum for making sauce-flavor liquor in China[J]. Biotechnol Bull, 2019, 35(5): 28-34.
[24]	中商情报网. 2020年贵州省酒用高粱市场供需形势及产量预测分析[EB/OL].(2020-7-22)[2022-12-03]. https://www.163.com/dy/article/FI5ICNRR051481OF.html.
	China Business Information Network. Market supply and demand situation and yield forecast analysis of wine sorghum in Guizhou province in 2020[EB/OL].(2020-7-22)[2022-12-03]. https://www.163.com/dy/article/FI5ICNRR051481OF.html.
[25]	丁延庆, 曹宁, 周棱波, 等. 酒用糯高粱EMS突变体库构建及突变体筛选[J]. 南方农业学报, 2020, 51(12): 2884-2891.
	Ding YQ, Cao N, Zhou LB, et al. Construction of EMS-induced mutant library and mutant screening in liquor-making waxy sorghum[J]. J South Agric, 2020, 51(12): 2884-2891.
[26]	郑海洋, 侯立龙, 曹富斌, 等. 大豆株高QTL定位及候选基因挖掘[J/OL]. 中国油料作物学报, 2022. DOI: 10.19802/j.issn.1007-9084.2022065. doi: 10.19802/j.issn.1007-9084.2022065
	Zheng HY, Hou LL, Cao FB, et al. Soybean plant height QTL mapping and candidate gene mining[J/OL]. Chin J Oil Crop Sci, 2022. DOI: 10.19802/j.iSSN.1007-9084.2022065. doi: 10.19802/j.iSSN.1007-9084.2022065
[27]	Zhao J, Mantilla Perez MB, Hu JY, et al. Genome-wide association study for nine plant architecture traits in Sorghum[J]. Plant Genome, 2016, 9(2): plantgenome2015.06.0044.
[8]	王丽华, 陆叶飞, 陆以静, 等. “高粱不育系Tx623A×苏丹草Sa”RIL群体农艺性状的QTL定位[J]. 山西农业科学, 2021, 49(12): 1491-1496.
	Wang LH, Lu YF, Lu YJ, et al. QTL mapping of the agronomic traits using an RIL populations of “Tx623A × sa”[J]. J Shanxi Agric Sci, 2021, 49(12): 1491-1496.
[9]	Zou GH, Zhai GW, Feng Q, et al. Identification of QTLs for eight agronomically important traits using an ultra-high-density map based on SNPs generated from high-throughput sequencing in sorghum under contrasting photoperiods[J]. J Exp Bot, 2012, 63(15): 5451-5462. doi: 10.1093/jxb/ers205 pmid: 22859680
[10]	Kajiya-Kanegae H, Takanashi H, Fujimoto M, et al. RAD-seq-based high-density linkage map construction and QTL mapping of biomass-related traits in sorghum using the Japanese Landrace takakibi NOG[J]. Plant Cell Physiol, 2020, 61(7): 1262-1272. doi: 10.1093/pcp/pcaa056 pmid: 32353144
[11]	Takanashi H, Shichijo M, Sakamoto L, et al. Genetic dissection of QTLs associated with spikelet-related traits and grain size in sorghum[J]. Sci Rep, 2021, 11(1): 9398. doi: 10.1038/s41598-021-88917-x pmid: 33931706
[12]	Brown PJ, Rooney WL, Franks C, et al. Efficient mapping of plant height quantitative trait loci in a sorghum association population with introgressed dwarfing genes[J]. Genetics, 2008, 180(1): 629-637. doi: 10.1534/genetics.108.092239 pmid: 18757942
[13]	Morris GP, Ramu P, Deshpande SP, et al. Population genomic and genome-wide association studies of agroclimatic traits in sorghum[J]. Proc Natl Acad Sci USA, 2013, 110(2): 453-458. doi: 10.1073/pnas.1215985110 pmid: 23267105
[14]	Hirano K, Kawamura M, Araki-Nakamura S, et al. Sorghum DW1 positively regulates brassinosteroid signaling by inhibiting the nuclear localization of BRASSINOSTEROID INSENSITIVE 2[J]. Sci Rep, 2017, 7(1): 126. doi: 10.1038/s41598-017-00096-w pmid: 28273925
[15]	Hilley JL, Weers BD, Truong SK, et al. Sorghum Dw2 encodes a protein kinase regulator of stem internode length[J]. Sci Rep, 2017, 7(1): 4616. doi: 10.1038/s41598-017-04609-5 pmid: 28676627
[16]	Li X, Li XR, Fridman E, et al. Dissecting repulsion linkage in the dwarfing gene Dw3 region for sorghum plant height provides insights into heterosis[J]. Proc Natl Acad Sci USA, 2015, 112(38): 11823-11828. doi: 10.1073/pnas.1509229112 pmid: 26351684
[28]	Hart GE, Schertz KF, Peng Y, et al. Genetic mapping of Sorghum bicolor(L.) Moench QTLs that control variation in tillering and other morphological characters[J]. Theor Appl Genet, 2001, 103(8): 1232-1242. doi: 10.1007/s001220100582 URL
[29]	Otomo K, Kenmoku H, Oikawa H, et al. Biological functions of ent- and syn-copalyl diphosphate synthases in rice: key enzymes for the branch point of gibberellin and phytoalexin biosynthesis[J]. PlantJ, 2004, 39(6): 886-893.
[30]	Bensen RJ, Johal GS, Crane VC, et al. Cloning and characterization of the maize An1 gene[J]. Plant Cell, 1995, 7(1): 75-84. doi: 10.1105/tpc.7.1.75 pmid: 7696880
[31]	Shiringani AL, Frisch M, Friedt W. Genetic mapping of QTLs for sugar-related traits in a RIL population of Sorghum bicolor L. Moench[J]. Theor Appl Genet, 2010, 121(2): 323-336. doi: 10.1007/s00122-010-1312-y pmid: 20229249
[32]	Liu HH, Liu HQ, Zhou LN, et al. Genetic architecture of domestication- and improvement-related traits using a population derived from Sorghum virgatum and Sorghum bicolor[J]. Plant Sci, 2019, 283: 135-146. doi: 10.1016/j.plantsci.2019.02.013 URL
[33]	Felderhoff TJ, Murray SC, Klein PE, et al. QTLs for energy-related traits in a sweet × grain sorghum[Sorghum bicolor(L.) Moench]mapping population[J]. Crop Sci, 2012, 52(5): 2040-2049. doi: 10.2135/cropsci2011.11.0618 URL
[34]	Nagai K, Mori Y, Ishikawa S, et al. Antagonistic regulation of the gibberellic acid response during stem growth in rice[J]. Nature, 2020, 584(7819): 109-114. doi: 10.1038/s41586-020-2501-8
[35]	Schmitz AJ, Begcy K, Sarath G, et al. Rice Ovate Family Protein 2(OFP2)alters hormonal homeostasis and vasculature development[J]. Plant Sci, 2015, 241: 177-188. doi: 10.1016/j.plantsci.2015.10.011 pmid: 26706069
[36]	Cai YH, Chen XJ, Xie K, et al. Dlf1, a WRKY transcription factor, is involved in the control of flowering time and plant height in rice[J]. PLoS One, 2014, 9(7): e102529.
[37]	Shehzad T, Okuno K. QTL mapping for yield and yield-contributing traits in sorghum(Sorghum bicolor(L.)Moench)with genome-based SSR markers[J]. Euphytica, 2015, 203(1): 17-31. doi: 10.1007/s10681-014-1243-9 URL
[17]	陆平. 高粱种质资源描述规范和数据标准[M]. 北京: 中国农业出版社, 2006.
	Lu P. Descriptors and data standard for sorghum[Sorghum bicolor(L.) Moench][M]. Beijing: China Agriculture Press, 2006.
[18]	曹永策, 李曙光, 张新草, 等. 夏大豆重组自交系群体遗传图谱构建及开花期QTL分析[J]. 中国农业科学, 2020, 53(4): 683-694. doi: 10.3864/j.issn.0578-1752.2020.04.002
	Cao YC, Li SG, Zhang XC, et al. Construction of genetic map and mapping QTL for flowering time in a summer planting soybean recombinant inbred line population[J]. Sci Agric Sin, 2020, 53(4): 683-694. doi: 10.3864/j.issn.0578-1752.2020.04.002
[19]	Murray MG, Thompson WF. Rapid isolation of high molecular weight plant DNA[J]. Nucleic Acids Res, 1980, 8(19): 4321-4325. doi: 10.1093/nar/8.19.4321 pmid: 7433111
[20]	Qi P, Gimode D, Saha D, et al. UGbS-Flex, a novel bioinformatics pipeline for imputation-free SNP discovery in polyploids without a reference genome: finger millet as a case study[J]. BMC Plant Biol, 2018, 18(1): 117. doi: 10.1186/s12870-018-1316-3 pmid: 29902967
[21]	丁延庆, 徐建霞, 汪灿, 等. 基于Super-GBS技术的高粱籽粒酿造相关性状QTL定位[J]. 核农学报, 2023, 37(2): 241-250. doi: 10.11869/j.issn.1000-8551.2023.02.0241
[38]	林泽川, 曹立勇. 水稻株型相关基因的定位与克隆研究进展[J]. 中国稻米, 2014, 20(1): 17-22, 27. doi: 10.3969/j.issn.1006-8082.2014.01.004
	Lin ZC, Cao LY. Progress on mapping and cloning of genes related to rice plant type[J]. China Rice, 2014, 20(1): 17-22, 27.
[39]	王文秀, 王磊. 玉米矮杆基因研究进展[J]. 生物技术通报, 2018, 34(11): 22-26. doi: 10.13560/j.cnki.biotech.bull.1985.2018-0444 URL
	Wang WX, Wang L. Research progress on maize dwarf genes[J]. Biotechnol Bull, 2018, 34(11): 22-26.
[40]	吕广德, 靳雪梅, 郭营, 等. 小麦株高分子遗传学研究进展[J]. 植物遗传资源学报, 2021, 22(3): 571-582. doi: 10.13430/j.cnki.jpgr.20200927001
	Lyu GD, Jin XM, Guo Y, et al. Advances in molecular genetics of wheat plant height[J]. J Plant Genet Resour, 2021, 22(3): 571-582. doi: 10.13430/j.cnki.jpgr.20200927001
[41]	Ge FY, Xie P, Wu YR, et al. Genetic architecture and molecular regulation of sorghum domestication[J]. aBIOTECH, 2022: 1-15.
[42]	Hao HQ, Li ZG, Leng CY, et al. sorghum breeding in the genomic era: opportunities and challenges[J]. Theor Appl Genet, 2021, 134(7): 1899-1924. doi: 10.1007/s00122-021-03789-z pmid: 33655424

性状 Trait	环境 Environment	亲本Parents		RIL群体RIL population
性状 Trait	环境 Environment	BTx623	红缨子 Hongyingzi	最小值 Minimum	最大值 Maximum	平均值 Mean	标准差 SD	变异系数 CV/%	偏度 Skewness	峰度 Kurtosis
株高 PH/cm	2020GY	120.33	266.33	101.00	360.67	207.37	56.94	27.46	0.176	-0.769
	2020AS	132.67	284.00	106.67	320.33	197.99	47.66	24.07	0.192	-0.773
	2020LD	122.00	196.33	81.67	254.00	178.02	31.65	17.78	-0.213	-0.453
	2021GY	124.33	215.00	105.00	316.67	201.16	43.32	21.53	0.070	-0.513
	2021AS	147.00	238.67	107.33	321.67	196.15	42.99	21.92	0.188	-0.671
节间数 IN	2020GY	8.67	10.67	5.67	13.33	9.73	1.19	12.22	0.144	0.404
	2020AS	7.67	10.33	6.00	12.67	8.75	1.27	14.52	0.509	-0.248
	2020LD	7.00	9.33	4.67	11.00	7.48	0.98	13.07	0.402	1.609
	2021GY	7.00	8.67	5.33	11.00	8.19	0.98	12.02	0.016	0.673
	2021AS	7.00	9.67	5.33	12.67	8.49	1.41	16.64	0.377	-0.087

性状 Trait	环境 Environment	亲本Parents		RIL群体RIL population
性状 Trait	环境 Environment	BTx623	红缨子 Hongyingzi	最小值 Minimum	最大值 Maximum	平均值 Mean	标准差 SD	变异系数 CV/%	偏度 Skewness	峰度 Kurtosis
株高 PH/cm	2020GY	120.33	266.33	101.00	360.67	207.37	56.94	27.46	0.176	-0.769
	2020AS	132.67	284.00	106.67	320.33	197.99	47.66	24.07	0.192	-0.773
	2020LD	122.00	196.33	81.67	254.00	178.02	31.65	17.78	-0.213	-0.453
	2021GY	124.33	215.00	105.00	316.67	201.16	43.32	21.53	0.070	-0.513
	2021AS	147.00	238.67	107.33	321.67	196.15	42.99	21.92	0.188	-0.671
节间数 IN	2020GY	8.67	10.67	5.67	13.33	9.73	1.19	12.22	0.144	0.404
	2020AS	7.67	10.33	6.00	12.67	8.75	1.27	14.52	0.509	-0.248
	2020LD	7.00	9.33	4.67	11.00	7.48	0.98	13.07	0.402	1.609
	2021GY	7.00	8.67	5.33	11.00	8.19	0.98	12.02	0.016	0.673
	2021AS	7.00	9.67	5.33	12.67	8.49	1.41	16.64	0.377	-0.087

性状Trait	2020GY-PH	2020AS-PH	2020SY-PH	2021GY-PH	2021AS-PH	2020GY-IN	2020AS-IN	2020SY-IN	2021GY-IN	2021AS-IN
2020GY-PH	1.000
2020AS-PH	0.832**	1.000
2020SY-PH	0.884**	0.783**	1.000
2021GY-PH	0.860**	0.826**	0.856**	1.000
2021AS-PH	0.844**	0.760**	0.814**	0.861**	1.000
2020GY-IN	0.474**	0.457**	0.387**	0.418**	0.381**	1.000
2020AS-IN	0.399**	0.584**	0.317**	0.383**	0.380**	0.651**	1.000
2020SY-IN	0.431**	0.422**	0.491**	0.428**	0.367**	0.671**	0.500**	1.000
2021GY-IN	0.380**	0.472**	0.302**	0.472**	0.390**	0.684**	0.665**	0.575**	1.000
2021AS-IN	0.475**	0.512**	0.432**	0.515**	0.618**	0.567**	0.633**	0.508**	0.599**	1.000

性状Trait	2020GY-PH	2020AS-PH	2020SY-PH	2021GY-PH	2021AS-PH	2020GY-IN	2020AS-IN	2020SY-IN	2021GY-IN	2021AS-IN
2020GY-PH	1.000
2020AS-PH	0.832**	1.000
2020SY-PH	0.884**	0.783**	1.000
2021GY-PH	0.860**	0.826**	0.856**	1.000
2021AS-PH	0.844**	0.760**	0.814**	0.861**	1.000
2020GY-IN	0.474**	0.457**	0.387**	0.418**	0.381**	1.000
2020AS-IN	0.399**	0.584**	0.317**	0.383**	0.380**	0.651**	1.000
2020SY-IN	0.431**	0.422**	0.491**	0.428**	0.367**	0.671**	0.500**	1.000
2021GY-IN	0.380**	0.472**	0.302**	0.472**	0.390**	0.684**	0.665**	0.575**	1.000
2021AS-IN	0.475**	0.512**	0.432**	0.515**	0.618**	0.567**	0.633**	0.508**	0.599**	1.000

性状 Trait	均方 Mean square			F值F value			广义遗传率 h²_B/%
性状 Trait	基因型Genotype	环境Environment	基因型iro G×E	基因型Genotype	环境Environment	基因型iro G×E	广义遗传率 h²_B/%
株高PH	26 001.18	75 159.27	1 238.43	224.52**	649.01**	10.69**	95.23
节间数IN	14.05	419.71	1.70	43.24**	1 291.97**	5.23**	85.78