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作物学报 ›› 2020, Vol. 46 ›› Issue (9): 1380-1387.doi: 10.3724/SP.J.1006.2020.94200

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

基于侯选基因标记的四倍体马铃薯休眠QTL关联分析

李竟才1,2(), 王强林3, 宋威武4, 黄维1, 肖桂林1, 吴承金4, 顾钦2, 宋波涛1,*()   

  1. 1 华中农业大学园艺林学学院 / 园艺植物生物学教育部重点实验室 / 农业农村部马铃薯生物学与生物技术重点实验室, 湖北武汉 430070
    2 黄冈师范学院生物与农业资源学院 / 大别山特色资源开发湖北省协同创新中心 / 经济林木种质改良与资源综合利用湖北省重点实验室, 湖北黄冈 438000
    3 黄冈市现代农业展示与信息中心, 湖北黄冈 438000
    4 恩施土家族苗族自治州农业科学院, 湖北 恩施 445000
  • 收稿日期:2019-12-18 接受日期:2020-03-24 出版日期:2020-09-12 网络出版日期:2020-04-17
  • 通讯作者: 宋波涛
  • 作者简介:E-mail: lijingcai@hgnu.edu.cn
  • 基金资助:
    本研究由国家现代农业产业技术体系(马铃薯)建设专项(CARS-09-P07);湖北省自然科学基金项目(2017CFB547);教育部大学生创新训练项目资助(201510514006)

Association analysis of dormancy QTL in tetraploid potato via candidate gene markers

LI Jing-Cai1,2(), WANG Qiang-Lin3, SONG Wei-Wu4, HUANG Wei1, XIAO Gui-Lin1, WU Cheng-Jin4, GU Qin2, SONG Bo-Tao1,*()   

  1. 1 College of Horticulture and Forestry Sciences, Huazhong Agricultural University / Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs / Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan 430070, Hubei, China
    2 College of Biology and Agricultural Resources, Huanggang Normal University / Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains / Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Huanggang 438000, Hubei, China
    3 Huanggang Modern Agriculture Exhibition and Information Center, Huanggang 438000, Hubei, China
    4 Academy of Agricultural Sciences of Enshi Tujia and Miao Autonomous Prefecture, Enshi 445000, Hubei, China
  • Received:2019-12-18 Accepted:2020-03-24 Published:2020-09-12 Published online:2020-04-17
  • Contact: Bo-Tao SONG
  • Supported by:
    China Agriculture Research System (Potato)(CARS-09-P07);Natural Science Foundation of Hubei Province(2017CFB547);Innovative Training Program for College Students of the Ministry of Education(201510514006)

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摘要：

休眠期是马铃薯(Solanum tuberosum L.)重要的块茎性状之一, 寻找调控马铃薯块茎休眠的关键基因, 揭示其分子机制以选育具有适宜休眠期长度的马铃薯品种, 对于解决当前马铃薯产业中过长或过短休眠期带来的经济损失和食品安全隐患等问题十分关键。前期研究在二倍体马铃薯连锁群体中定位了6个加性休眠QTL, 本研究拟在四倍体马铃薯育种材料中验证这些休眠QTL。基于休眠QTL连锁的候选基因标记, 采用混合线性模型(MLM), 模型中考虑群体结构和亲缘关系(Q+K), 在四倍体马铃薯自然群体St-hzau中对马铃薯块茎休眠期进行了关联分析。5号染色体上休眠QTL DorB5.3连锁的候选基因标记S199_300和GWD (根据葡聚糖水双激酶α-glucan water dikinase基因设计)与马铃薯块茎休眠期具有显著的关联(P<0.05), 分别解释了休眠期表型变异的7.8%和3.2%, 分别能增加休眠期7.1 d和4.5 d, 即在二倍体马铃薯连锁群体中定位的稳定主效休眠QTL DorB5.3在四倍体马铃薯关联群体St-hzau中也表现显著, DorB5.3的稳定性在关联分析结果中得到了验证, 表明候选基因标记策略在马铃薯块茎休眠QTL关联分析中是一种有效的策略。本研究所验证的主效休眠QTL DorB5.3及相应连锁标记可以直接用于马铃薯休眠育种。据此可以推测GWD可能在控制还原糖含量和块茎休眠2个方面均发挥作用, 马铃薯块茎休眠机制与还原糖含量变化机制可能存在着部分交叉。

关键词: 马铃薯, 休眠, QTL, 候选基因, 关联分析

Abstract:

Dormancy is one of the prominent and important potato (Solanum tuberosum L.) tuber traits. Identifying the key genes regulated potato tuber dormancy and revealing its molecular mechanism to select potato varieties with desirable dormancy length are crucial to solve the economic losses and food safety issues due to the unsuitable dormancy length in potato industry. Previously, six additive dormancy QTLs were mapped in a linkage population of diploid potato. This study aimed to verify these QTLs in tetraploid potato breeding germplasm. Based on the candidate gene markers linked to the dormancy QTLs, we used a mixed linear model (MLM), taking the population structure and genetic relationship (Q+K) into account to conduct the association analysis of potato tuber dormancy in a natural tetraploid potato population St-hzau. The candidate gene markers S199_300 and GWD (derived from α-glucan water dikinase gene) linked to QTL DorB5.3 on chromosome 5 showed significant association with potato tuber dormancy (P < 0.05), which explained 7.8% and 3.2% of the phenotypic variation, respectively. The two markers could increase the dormancy length by 7.1 d and 4.5 d, respectively, revealing that the main effect of dormancy QTL DorB5.3 in the linkage population of diploid potato was also significant in the natural tetraploid potato population St-hzau. So the stability of DorB5.3 was validated in the association analysis, showing that the candidate gene marker strategy is an effective strategy in QTL association analysis of potato tuber dormancy. The major dormancy QTL DorB5.3 and corresponding linkage markers verified in this study could be directly used in potato dormancy breeding. According to the results, it could be proposed that GWD might play a role in controlling reducing-sugar content and dormancy of potato tuber, indicating a mechanism crosstalk between potato tuber dormancy and reducing-sugar content.

Key words: Solanum tuberosum, dormancy, QTL, candidate gene, association analysis

表1

3个环境中马铃薯关联群体St-hzau种植和收获日期"

环境
Environment		 地点
Location		 种植日期
Planting date		 收获日期
Harvest date
I 武汉Wuhan 2015-01-15 2015-05-20
II 武汉Wuhan 2016-01-22 2016-06-04
III 长阳Changyang 2016-03-10 2016-07-20

表2

候选基因标记引物"

引物名称a
Primer name a		 染色体
Chr.		 连锁QTL
Linked QTL		 上游引物
Forward primer (5°-3°)		 下游引物
Reverse primer (5°-3°)		 退火温度
Annealing
temperature (℃)
S199 Chr05 DorB5.3 TGCCTACTGCCCAAAACATT ACTGGCTGGGAAGCATACAC 55
GWD Chr05 DorB5.3 TCCATCCTGAGACTGGAGATAC ACTTGTACTGCAGGACTGGAAG 60
G6pt Chr05 DorB5.3 GGCTCACACAATTGGTCATGTG CCAAGATTGCAATAGCAGCACC 60
s1939 Chr05 DorB5.3 TGAGATACTTTGTGTGCTCC AAATTGGTTTTCCAGATTGA 56
STI058 Chr05 DorB5.3 CAAGCACGTTACAACAAGCAA TTGAAGCATCACATACACAAACA 60-54
FK Chr06 DorB6.3 GCTTTGGCGTTCGTGACTCTAC AGTGGTGTCAACAGTCTTCACG 60
S1711 Chr06 DorE6.17 TTCTTCAGGGTCCTCTTTCGG AGTGCTTCCTCGCATGGGATT 67
S1614 Chr06 DorE6.17, DorE6.19 TCGTGGGTCAAGGTTGTTCAT ATGGTGGATTAGACCTAGTTGCTG 65
Dpe-P Chr04 DorE4.6 CACTACTTTTCAATCTCCTATCCC GCATAGTCACGAACTTTTTTCC 56
α-Glu Chr04 DorE4.6 ACCAAGCTGTGGTTAACCAGAG GCAGTTGCGAATAACTGTGGCA 60
Ppe Chr03 DorB3.17 TCCGTCCATCCTTTCTGCTAAC AACTCCACCATCAACTTCAATC 57

图1

关联群体St-hzau马铃薯块茎休眠期表型分布 图中I、II和III分别对应于表1所列3个田间环境。"

表3

3个环境中马铃薯块茎休眠期"

环境a
Environment a		 块茎发芽起始日期
First sprouting date		 平均值
Mean		 标准差
Standard deviation		 方差
Variance		 偏度
Skewness		 峰度
Kurtosis
I 2015-07-01 86.413 21.032 432.721 0.077 0.843
II 2016-07-10 68.000 12.000 134.400 0.181 -0.783
III 2016-08-26 85.963 15.647 240.295 0.382 -0.456

图2

St-hzau群体结构 关联群体St-hzau划分为A、B和C三个亚群体。"

图3

候选基因标记与马铃薯块茎休眠QTL 第1个连锁群顶部的Chr04E表示母本ED25 (E)的4号染色体, Chr03B表示父本S. berthaultii acc CW2-1 (B)的3号染色体。最左边连锁群标尺的单位是cM。无休眠QTL的其他染色体此处省略, 详见Xiao等[23]的研究。标记位于连锁群的右侧, 休眠QTL的位置在连锁群的左侧。[*]突出显示chr05B上在马铃薯关联群体St-hzau中与块茎休眠期有显著关联的标记, 其他候选基因标记下画线标出。"

[1] 王鹏, 连勇, 金黎平. 马铃薯块茎休眠及萌发过程中几种酶活性变化. 华北农学报, 2003,18(1):33-36.
Wang P, Lian Y, Jin L P. The research on the regulation of enzymes during dormancy and dormancy releasing. Acta Agric Boreali-Sin, 2003,18(1):33-36 (in Chinese with English abstract).
[2] 司怀军, 张宁, 刘柏林, 文义凯, 唐勋, 杨江伟, 周香艳. 马铃薯块茎休眠与发芽性状调控的分子基础研究. 见: 2017年马铃薯大会主编. 马铃薯产业与精准扶贫. 哈尔滨: 哈尔滨地图出版社, 2017. pp 177-182.
Si H J, Zhang N, Liu B L, Wen Y K, Tang X, Yang J W, Zhou X Y. Molecular basic study on the regulation of dormancy and germination of potato tubers. In: 2017 Potato Conference, eds. Potato Industry and Precise Poverty Alleviation. Harbin: Harbin Cartographic Press, 2017. pp 177-182(in Chinese).
[3] Koornneef M, Bentsink L, Hilhorst H. Seed dormancy and germination. Curr Opin Plant Biol, 2002,5:33-36.
doi: 10.1016/s1369-5266(01)00219-9 pmid: 11788305
[4] Bisognin D, Manrique-Carpintero N, Douches D. QTL analysis of tuber dormancy and sprouting in potato. Am J Potato Res, 2018,95:374-382.
doi: 10.1007/s12230-018-9638-0
[5] Freyre R, Warnke S, Sosinski B, Douches D. Quantitative trait locus analysis of tuber dormancy in diploid potato (Solanum spp.). Theor Appl Genet, 1994,89:474-480.
doi: 10.1007/BF00225383 pmid: 24177897
[6] Naz R, Li M, Ramzan S, Li G, Liu J, Cai X, Xie C. QTL mapping for microtuber dormancy and GA3 content in a diploid potato population. Biol Open, 2018, 7: bio027375.
doi: 10.1242/bio.039362 pmid: 30404898
[7] Sliwka J, Wasilewicz-Flis I, Jakuczun H, Gebhardt C. Tagging quantitative trait loci for dormancy, tuber shape, regularity of tuber shape, eye depth and flesh colour in diploid potato originated from sixSolanum species. Plant Breed, 2008,127:49-55.
[8] Simko I, McMurry S, Yang H, Manschot A, Davies P, Ewing E. Evidence from polygene mapping for a causal relationship between potato tuber dormancy and abscisic acid content. Plant Physiol, 1997,115:1453-1459.
doi: 10.1104/pp.115.4.1453 pmid: 12223876
[9] Van den Berg J, Ewing E, Plaisted R, McMurry S, Bonierbale M. QTL analysis of potato tuber dormancy. Theor Appl Genet, 1996,93:317-324.
doi: 10.1007/BF00223171 pmid: 24162286
[10] Li J, Huang W, Cao H, Xiao G, Zhou J, Xie C, Xia J, Song B. Additive and epistatic QTLs underlying the dormancy in a diploid potato population across seven environments. Sci Hortic, 2018,240:578-584.
[11] Thornsberry J, Goodman M, Doebley J, Kresovich S, Nielsen D, Buckler E. Dwarf8 polymorphisms associate with variation in flowering time. Nat Genet, 2001,28:286-289.
doi: 10.1038/90135 pmid: 11431702
[12] 田润苗, 张雪海, 汤继华, 白光红, 付志远. 玉米种子萌发相关性状的全基因组关联分析. 作物学报, 2018,44:672-685.
Tian R M, Zhang X H, Tang J H, Bai G H, Fu Z Y. Genome-wide association studies of seed germination related traits in maize. Acta Agron Sin, 2018,44:672-685 (in Chinese with English abstract) .
[13] 霍强, 杨鸿, 陈志友, 荐红举, 曲存民, 卢坤, 李加纳. 基于QTL定位和全基因组关联分析筛选甘蓝型油菜株高和一次有效分枝高度的候选基因. 作物学报, 2020,46:214-227.
Huo Q, Yang H, Chen Z Y, Jian H J, Qu C M, Lu K, Li J N. Candidate genes screening for plant height and the first branch height based on QTL mapping and genome-wide association study in rapessed (Brassica napus L.). Acta Agron Sin, 2020,46:214-227 (in Chinese with English abstract) .
[14] 邹伟伟, 路雪丽, 王丽, 薛大伟, 曾大力, 李志新. 不同氮水平下水稻钾吸收及全基因组关联分析. 作物学报, 2019,45:1189-1199.
Zou W W, Lu X L, Wang L, Xue D W, Zeng D L, Li Z X. Potassium uptake and genome-wide association analysis of rice under different nitrogen levels. Acta Agron Sin, 2019,45:1189-1199 (in Chinese with English abstract) .
[15] D'Hoop B, Keizer P, Paulo M, Visser R, van Eeuwijk F, van Eck H. Identification of agronomically important QTL in tetraploid potato cultivars using a marker-trait association analysis. Theor Appl Genet, 2014,127:731-748.
pmid: 24408376
[16] Khlestkin V, Rozanova I, Efimov V, Khlestkina E. Starch phosphorylation associated SNPs found by genome-wide association studies in the potato (Solanum tuberosum L.). BMC Genet, 2019,20:29.
doi: 10.1186/s12863-019-0729-9 pmid: 30885119
[17] Klaassen M, Willemsen J, Vos P, Visser R, van Eck H, Maliepaard C, Trindade L. Genome-wide association analysis in tetraploid potato reveals four QTLs for protein content. Mol Breed, 2019,39:151.
doi: 10.1007/s11032-019-1070-8
[18] Li L, Paulo M, Strahwald J, Lübeck J, Hofferbert H, Tacke E, Junghans H, Wunder J, Draffehn A, van Eeuwijk F, Gebhardt C. Natural DNA variation at candidate loci is associated with potato chip color, tuber starch content, yield and starch yield. Theor Appl Genet, 2008,116:1167-1181.
doi: 10.1007/s00122-008-0746-y
[19] Van Ittersum M, Aben F, Keijzer C. Morphological changes in tuber buds during dormancy and initial sprout growth of seed potatoes. Potato Res, 1992,35:249-260.
[20] Liu B, Zhang N, Wen Y, Jin X, Yang J, Si H, Wang D. Transcriptomic changes during tuber dormancy release process revealed by RNA sequencing in potato. J Biotechnol, 2015,198:17-30.
doi: 10.1016/j.jbiotec.2015.01.019 pmid: 25661840
[21] Dellaporta S, Jonathan W, Hicks J. A plant DNA minipreparation: version II. Plant Mol Biol Rep, 1983,1:19-21.
[22] Li J, Lindqvist-Kreuze H, Tian Z, Liu J, Song B, Landeo J, Portal L, Gastelo M, Frisancho J, Sanchez L, Meijer D, Xie C, Bonierbale M. Conditional QTL underlying resistance to late blight in a diploid potato population. Theor Appl Genet, 2012,124:1339-1350.
[23] Xiao G, Huang W, Cao H, Tu W, Wang H, Zheng X, Liu J, Song B, Xie C. Genetic loci conferring reducing sugar accumulation and conversion of cold-stored potato tubers revealed by QTL analysis in a diploid population. Front Plant Sci, 2018,9:315.
doi: 10.3389/fpls.2018.00315 pmid: 29593769
[24] Han Y, Teng C, Hu Z, Song Y. An optimal method of DNA silver staining in polyacrylamide gels. Electrophoresis, 2008,29:1355-1358.
[25] Pritchard J, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics, 2000,155:945-959.
pmid: 10835412
[26] Earl D, von Holdt B. STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour, 2012,4:359-361.
[27] Bradbury P, Zhang Z, Kroon D, Casstevens T, Ramdoss Y, Buckler E. TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics, 2007,23:2633-2635.
[28] Zhang Z, Ersoz E, Lai C, Todhunter R, Tiwari H, Gore M, Bradbury P, Yu J, Arnett D, Ordovas J, Buckler E S. Mixed linear model approach adapted for genome-wide association studies. Nat Genet, 2010,42:355-360.
pmid: 20208535
[29] Voorrips R. MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered, 2002,93:77-78.
[30] Suttle J. Physiological regulation of potato tuber dormancy. Am J Potato Res, 2004,81:253-262.
[31] Vreugdenhil D. The canon of potato science: dormancy. Potato Res, 2007,50:371-373.
[32] Hou J, Liu T, Reid S, Zhang H, Peng X, Sun K, Dua J, Sonnewald U, Song B. Silencing of α-amylase StAmy23 in potato tuber leads to delayed sprouting. Plant Physiol Biochem, 2019,139:411-418.
[33] Ritter G, Lloyd J, Eckermann N, Rottmann A, Kossmann J, Steup M. The starch-related R1 protein is an alpha-glucan, water dikinase. Proc Natl Acad Sci USA, 2002,99:7166-7171.
pmid: 12011472
[34] Mikkelsen R, Mutenda K, Mant A, Schurmann P, Blennow A. Alpha-glucan, water dikinase (GWD): a plastidic enzyme with redox-regulated and coordinated catalytic activity and binding affinity. Proc Natl Acad Sci USA, 2005,102:1785-1790.
doi: 10.1073/pnas.0406674102 pmid: 15665090
[35] Lorberth R, Ritte G, Willmitzer L, Kossmann J. Inhibition of a starch-granule-bound protein leads to modified starch and repression of cold sweetening. Nat Biotechnol, 1998,16:473-477.
pmid: 9592398
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