Welcome to Acta Agronomica Sinica,

Acta Agronomica Sinica ›› 2020, Vol. 46 ›› Issue (9): 1380-1387.doi: 10.3724/SP.J.1006.2020.94200

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

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 Online:2020-09-12 Published:2020-04-17
  • Contact: Bo-Tao SONG E-mail:lijingcai@hgnu.edu.cn;songbotao@mail.hzau.edu.cn
  • 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)

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

Table 1

Planting and harvest dates of potato association population St-hzau in three environments"

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

Table 2

Marker primers for candidate genes"

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

Fig. 1

Phenotypic distributions of potato tuber dormancy in the association population St-hzau In the figure, I, II, and III correspond to the three field environments listed in Table 1, respectively."

Table 3

Dormancy length of potato tubers in the three environments"

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

Fig. 2

Population structure of St-hzau The association population St-hzau was divided into three sub-populations."

Fig. 3

Candidate gene markers and potato tuber dormancy QTL Chr04E on the top of the first group indicates chromosome 4 of the maternal parent ED25 (E) and Chr03B indicates chromosome 3 of the paternal parent S. berthaultii acc. CW2-1 (B). The unit of the scale on the far left is cM for linkage groups. Chromosomes without dormancy QTL were omitted and they could be found in the research of Xiao et al. [23] The markers are on the right and locations of dormancy QTLs are on the left of the groups. Significant markers on Chr05B associated with tuber dormancy in potato association population St-hzau are highlighted by [*]. Other candidate gene markers are underlined."

[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
[1] HU Wen-Jing, LI Dong-Sheng, YI Xin, ZHANG Chun-Mei, ZHANG Yong. Molecular mapping and validation of quantitative trait loci for spike-related traits and plant height in wheat [J]. Acta Agronomica Sinica, 2022, 48(6): 1346-1356.
[2] TIAN Tian, CHEN Li-Juan, HE Hua-Qin. Identification of rice blast resistance candidate genes based on integrating Meta-QTL and RNA-seq analysis [J]. Acta Agronomica Sinica, 2022, 48(6): 1372-1388.
[3] YU Chun-Miao, ZHANG Yong, WANG Hao-Rang, YANG Xing-Yong, DONG Quan-Zhong, XUE Hong, ZHANG Ming-Ming, LI Wei-Wei, WANG Lei, HU Kai-Feng, GU Yong-Zhe, QIU Li-Juan. Construction of a high density genetic map between cultivated and semi-wild soybeans and identification of QTLs for plant height [J]. Acta Agronomica Sinica, 2022, 48(5): 1091-1102.
[4] HUANG Li, CHEN Yu-Ning, LUO Huai-Yong, ZHOU Xiao-Jing, LIU Nian, CHEN Wei-Gang, LEI Yong, LIAO Bo-Shou, JIANG Hui-Fang. Advances of QTL mapping for seed size related traits in peanut [J]. Acta Agronomica Sinica, 2022, 48(2): 280-291.
[5] ZHANG Yan-Bo, WANG Yuan, FENG Gan-Yu, DUAN Hui-Rong, LIU Hai-Ying. QTLs analysis of oil and three main fatty acid contents in cottonseeds [J]. Acta Agronomica Sinica, 2022, 48(2): 380-395.
[6] JIAN Hong-Ju, SHANG Li-Na, JIN Zhong-Hui, DING Yi, LI Yan, WANG Ji-Chun, HU Bai-Geng, Vadim Khassanov, LYU Dian-Qiu. Genome-wide identification and characterization of PIF genes and their response to high temperature stress in potato [J]. Acta Agronomica Sinica, 2022, 48(1): 86-98.
[7] XU De-Rong, SUN Chao, BI Zhen-Zhen, QIN Tian-Yuan, WANG Yi-Hao, LI Cheng-Ju, FAN You-Fang, LIU Yin-Du, ZHANG Jun-Lian, BAI Jiang-Ping. Identification of StDRO1 gene polymorphism and association analysis with root traits in potato [J]. Acta Agronomica Sinica, 2022, 48(1): 76-85.
[8] YU Rui-Su, TIAN Xiao-Kang, LIU Bin-Bin, DUAN Ying-Xin, LI Ting, ZHANG Xiu-Ying, ZHANG Xing-Hua, HAO Yin-Chuan, LI Qin, XUE Ji-Quan, XU Shu-Tu. Dissecting the genetic architecture of lodging related traits by genome-wide association study and linkage analysis in maize [J]. Acta Agronomica Sinica, 2022, 48(1): 138-150.
[9] ZENG Wei-Ying, LAI Zhen-Guang, SUN Zu-Dong, YANG Shou-Zhen, CHEN Huai-Zhu, TANG Xiang-Min. Identification of the candidate genes of soybean resistance to bean pyralid (Lamprosema indicata Fabricius) by BSA-Seq and RNA-Seq [J]. Acta Agronomica Sinica, 2021, 47(8): 1460-1471.
[10] ZHANG Bo, PEI Rui-Qing, YANG Wei-Feng, ZHU Hai-Tao, LIU Gui-Fu, ZHANG Gui-Quan, WANG Shao-Kui. Mapping and identification QTLs controlling grain size in rice (Oryza sativa L.) by using single segment substitution lines derived from IAPAR9 [J]. Acta Agronomica Sinica, 2021, 47(8): 1472-1480.
[11] LUO Lan, LEI Li-Xia, LIU Jin, ZHANG Rui-Hua, JIN Gui-Xiu, CUI Di, LI Mao-Mao, MA Xiao-Ding, ZHAO Zheng-Wu, HAN Long-Zhi. Mapping QTLs for yield-related traits using chromosome segment substitution lines of Dongxiang common wild rice (Oryza rufipogon Griff.) and Nipponbare (Oryza sativa L.) [J]. Acta Agronomica Sinica, 2021, 47(7): 1391-1401.
[12] CHEN Can, NONG Bao-Xuan, XIA Xiu-Zhong, ZHANG Zong-Qiong, ZENG Yu, FENG Rui, GUO Hui, DENG Guo-Fu, LI Dan-Ting, YANG Xing-Hai. Genome-wide association study of blast resistance loci in the core germplasm of rice landraces from Guangxi [J]. Acta Agronomica Sinica, 2021, 47(6): 1114-1123.
[13] HAN Yu-Zhou, ZHANG Yong, YANG Yang, GU Zheng-Zhong, WU Ke, XIE Quan, KONG Zhong-Xin, JIA Hai-Yan, MA Zheng-Qiang. Effect evaluation of QTL Qph.nau-5B controlling plant height in wheat [J]. Acta Agronomica Sinica, 2021, 47(6): 1188-1196.
[14] WANG Wu-Bin, TONG Fei, KHAN Mueen-Alam, ZHANG Ya-Xuan, HE Jian-Bo, HAO Xiao-Shuai, XING Guang-Nan, ZHAO Tuan-Jie, GAI Jun-Yi. Detecting QTL system of root hydraulic stress tolerance index at seedling stage in soybean [J]. Acta Agronomica Sinica, 2021, 47(5): 847-859.
[15] ZHOU Xin-Tong, GUO Qing-Qing, CHEN Xue, LI Jia-Na, WANG Rui. Construction of a high-density genetic map using genotyping by sequencing (GBS) for quantitative trait loci (QTL) analysis of pink petal trait in Brassica napus L. [J]. Acta Agronomica Sinica, 2021, 47(4): 587-598.
Viewed
Full text


Abstract

Cited

  Shared   
  Discussed   
No Suggested Reading articles found!