G.41×新疆野苹果树体生长性状的QTL精细定位及候选基因预测

doi:10.3864/j.issn.0578-1752.2018.11.013

摘要/Abstract

摘要： 【目的】矮化砧木可以诱导地上部接穗品种矮化，实现苹果的丰产和稳产。因此，深入挖掘调控苹果树体生长的基因，可以改善苹果树形，加强苹果园地的管理方便性。【方法】以矮化苹果砧木‘G.41’和乔化苹果砧木新疆野苹果（Malus sieversii）为亲本构建的188株F₁代分离群体为试材，并于每个分离群体植株上嫁接‘富士冠军’。基于SSR标记技术，采用Join Map 4.0作图软件构建苹果遗传连锁图，应用Map QTL 5.0作图软件，结合后代群体的表型数据，对接穗高度和接穗横截面积生长性状进行初步QTL定位。结合苹果基因组序列信息，利用Primer5.0软件进行新SSR标记开发，并对初步定位区域进行精细定位及候选基因预测。【结果】该研究从361对SSR引物中筛选出108对在亲本之间表现出多态的SSR引物，多态率为29.9%。其中95对引物用于遗传连锁图谱构建，并在5号连锁群上初步检测出4个与植株生长性状相关的QTL位点，与接穗高度、接穗横截面积性状紧密连锁的两个标记，为L05024和Hi09b04。根据初步定位区域的序列信息，设计了新的SSR引物24对，其中在亲本间表现出多态的有10对，利用该10对引物对5号连锁群重新分析。构建了包含21个SSR标记、总长为86.0 cM的高密度遗传图谱，其平均遗传距离为7.52 cM。通过对接穗高度与接穗横截面积生长相关性状的QTL分析，在SSR标记L05024和Hi09b04之间找到与其相关的QTL位点，其表型贡献率分别为19.2%和51.7%。将该QTL位点与基因组序列对比，发现其物理距离为543 kb，并且该QTL区间包含16个候选基因。推测其中MDP0000323212为与植株生长密切相关的基因。【结论】本研究将砧木诱导矮化基因定位于苹果第5号染色体543 kb区段内，侧翼标记分别为L05024和Hi09b04，其物理距离为4.048—4.591 Mb，并筛选到可能参与调控植株生长的候选基因MDP0000323212。

关键词: 苹果砧木, SSR, 遗传图谱, QTL, 候选基因

Abstract: 【Objective】Dwarf rootstock is an important germplasm to be utilized in the production of high and stable yields of apples by inducing dwarf scions. Mapping the genes that regulate the growth of apple trees has important theoretical and practical significance for improving apple's yield and quality. 【Method】 In this study, 188 F₁ progenies derived from the cross G.41×Malus sieversii were used to perform QTL mapping, and ‘Fuji Champion’ were grafted on every F₁plant. Subsequently, based on SSR markers, a genetic map of apple was constructed using Join Map 4.0 software. Using Map QTL 5.0 mapping software, the growth traits, including scion height and cross-sectional area of the scion were used as phenotypic data in QTL preliminary analysis. Combined with information from the apple genome sequence and newly developed SSR markers using Primer 5.0 software, the QTL has been defined and the candidate genes were predicted. 【Result】 In this study, a total of 108 out of 361 SSRs showed a variable degree of polymorphism, and the polymorphism rate was 29.9%. A genetic map was constructed using 95 of 108 polymorphism SSRs and four QTLs for the growth trait were detected in linkage group No.5. Two markers (L05024 and Hi09b04) were closely linked with the height and the cross-sectional area of scion. Combined with the genome sequence, 24 new SSR markers were developed, which contained 10 polymorphism markers. Subsequently, the linkage group No.5 was analyzed again using these 10 markers. The reconstructed high density linkage group, consisted of 21 SSR markers, spanning 86.0 cM with an average of 7.52 cM per marker. The QTLs responsible for the height and the cross-sectional area of the scion were defined and two relevant SSR markers (L05024 and Hi09b04) were identified accounting for 19.2% and 51.7% of the observed phenotypic variation. According to the ‘Gold Delicious’ genome sequence, this locus has been defined in a region of 543 kb that contains 16 candidate genes and a gene (MDP0000323212) was considered as the candidate gene for plant growth in this QTL interval. 【Conclusion】 In this study, genes responsible for dwarfing were located in a 4.048-4.591 Mb interval on apple chromosome No.5 and two high linked SSR markers (L05024 and Hi09b04) were identified. A gene (MDP0000323212) was identified as a potential candidate gene for growth traits.

Key words: apple rootstock, SSR, genetic map, QTL, candidate gene

董军，王京，梁微，马百全，董丽娟，马锋旺，符轩畅，李翠英. G.41×新疆野苹果树体生长性状的QTL精细定位及候选基因预测[J]. 中国农业科学, 2018, 51(11): 2155-2163.

DONG Jun, WANG Jing, LIANG Wei, MA BaiQuan, DONG LiJuan, MA FengWang, FU XuanChang, LI CuiYing. QTL Fine Mapping and Candidate Gene Prediction for Growth Traits in G.41×Malus sieversii[J]. Scientia Agricultura Sinica, 2018, 51(11): 2155-2163.

0
/ / 推荐

导出引用管理器 EndNote|Reference Manager|ProCite|BibTeX|RefWorks

链接本文: https://www.chinaagrisci.com/CN/10.3864/j.issn.0578-1752.2018.11.013

https://www.chinaagrisci.com/CN/Y2018/V51/I11/2155

参考文献

[1] LAURENS F. Review of the current apple breeding programes in the world: objectives for scion cultivar improvement. Eucarpia Symposium on Fruit Breeding and Genetics, 1996, 484: 163-170.

[2] 陈学森, 韩明玉, 苏桂林, 刘凤之, 过国南, 姜远茂, 毛志泉, 彭福田, 束怀瑞. 当今世界苹果产业发展趋势及我国苹果产业优质高效发展意见. 果树学报, 2010, 27(4): 598-604.

CHEN X S, HAN M Y, SU G L, LIU F Z, GUO G N, JIANG Y M, MAO Z Q, PENG F T, SHU H R. Discussion on today's world apple industry trends and the suggestions on sustainable and efficient development of apple industry in China. Journal of Fruit Science, 2010, 27(4): 598-604. (in Chinese)

[3] ATKINSON C, ELSE M. Understanding how rootstocks dwarf fruit trees. Compact Fruit Tree, 2001, 34(2): 46-49.

[4] SELEZNYOVA A N, THORP T G, WHITE M, TUSTIN S, COSTES E. Application of architectural analysis and AMAP mod methodology to study dwarfing phenomenon: The branch structure of ‘Royal Gala’ apple grafted on dwarfing and non-dwarfing rootstock/interstock combinations. Annals of Botany, 2003, 91(6): 665-672.

[5] LAURENS F, AUDERGON J M, CLAVERIE J, CLAVERIE J, DUVAL H, GERMAIN E, KERVELLA J, LESPINASSE J. Integration of architectural types in French programes of ligneous fruit species genetic improvement. Fruits-Paris, 2000, 55(2): 141-152.

[6] 李英慧, 韩振海, 许雪峰. 分子标记技术在苹果育种中的应用. 生物技术通报, 2002, 18(6): 11-14.

LI Y H, HAN Z H, XU X F. Application of molecular marker technique in apple breeding. Biotechnology Bulletin, 2002, 18(6): 11-14. (in Chinese)

[7] 过国南, 阎振立, 张顺妮. 我国建国以来苹果品种选育研究的回顾及今后育种的发展方向. 果树学报, 2003, 20(2): 127-134.

GUO G N, YAN Z L, ZHANG S N. Review and outlook of breeding in China. Journal of Fruit Science, 2003, 20(2): 127-134. (in Chinese)

[8] 王宇霖. 关于我国苹果育种研究工作的几点想法. 果树学报, 2008, 25(3): 559-565.

WANG Y L. Some ideas about the apple breeding in China. Journal of Fruit Science, 2008, 25(3): 559-565. (in Chinese)

[9] 黄金凤, 王冬梅, 闫忠业, 吕天星, 王颖答, 刘志. 苹果遗传图谱的构建与QTL定位研究进展. 江苏农业科学, 2016, 44(2): 4-8.

HUANG J F, WANG D M, YAN Z Y, LV T X, WANG Y D, LIU Z. Advance in genetic mapping and QTL localization of apple. Jiangsu Agricultural Sciences, 2016, 44(2): 4-8. (in Chinese)

[10] WATKINS R, SPANGELO L P S. Components of genetic variance for plant survival and vigor of apple trees. Theoretical and Applied Genetics, 1970, 40(5): 195-203.

[11] DUREL C E, LAURENS F, FOUILLET A, LESPINASSE Y. Utilization of pedigree information to estimate genetic parameters from large unbalanced data sets in apple. Theoretical and Applied Genetics, 1998, 96(8): 1077-1085.

[12] ORAGUZIE N C, HOFSTEE M E, BREWER L R, HOWARD C. Estimation of genetic parameters in a recurrent selection program in apple. Euphytica, 2001, 118(1): 29-37.

[13] PILCHER R L R, CELTON J M, GARDINER S E, TUSTIN D. S. Genetic markers linked to the dwarfing trait of apple rootstock ‘Malling 9’. Journal of the American Society for Horticultural Science, 2008, 133(1): 100-106.

[14] FAZIO G, WAN Y, KVIKLYS D, ROMERO L, ADAMS R, STRICKLAND D, ROBINSON T. Dw2, a new dwarfing locus in apple rootstocks and its relationship to induction of early bearing in apple scions. Journal of the American Society for Horticultural Science, 2014, 139(2): 87-98.

[15] FOSTER T M, CELTON J M, CHAGNÉ D, TUSTIN D S, GARDINER S E. Two quantitative trait loci, Dw1 and Dw2, are primarily responsible for rootstock-induced dwarfing in apple. Horticulture Research, 2015: 1-9.

[16] HARRISON N, HARRISON R J, BARBER-PEREZ N, CASCANT- LOPEZ E, COBO-MEDINA M, LIPSKA M, FERNÁNDEZ- FERNÁNDEZ F. A new three-locus model for rootstock- induced dwarfing in apple revealed by genetic mapping of root bark percentage. Journal of Experimental Botany, 2016, 67(6): 1871-1881.

[17] FERNÁNDEZ-FERNÁNDEZ F, ANTANAVICIUTE L, VAN DYK MM, TOBUTT K R, EVANS K M, REES D J G, SARGENT D J. A genetic linkage map of an apple rootstock progeny anchored to the Malus genome sequence. Tree Genetics & Genomes, 2012, 8(5): 991-1002.

[18] 何坤辉, 常立国, 崔婷婷, 渠建洲, 郭东伟, 徐淑兔. 多环境下玉米株高和穗位高的QTL定位. 中国农业科学, 2016, 49(8): 1443-1452.

HE K H, CHANG L G, CUI T T , QU J Z, GUO D W, XU S T. Mapping QTL for plant height and ear height in maize under multi- environments. Scientia Agricultura Sinica, 2016, 49(8): 1443-1452.

[19] 张江江, 詹杰鹏, 刘清云, 师家勤, 王新发, 刘贵华. 油菜株高qtl定位、整合和候选基因鉴定. 中国农业科学, 2017, 50(17): 3247-3258.

ZHANG J J, ZHAN J P, LIU Q Y, SHI J Q, WANG X F, LIU G H. QTL mapping and integration as well as candidate genes identification for plant height in rapeseed (Brassica napus L.). Scientia Agricultura Sinica, 2017, 50(17): 3247-3258.

[20] 姚晓云, 李清, 刘进, 姜树坤, 杨生龙,王嘉宇. 不同环境下水稻株高和穗长的QTL分析. 中国农业科学, 2015, 48(3): 407-414.

YAO X Y, LI Q, LIU J, JIANG S K, YANG S L, WANG J Y. Dissection of QTLs for plant height and panicle length traits in rice under different environment. Scientia Agricultura Sinica, 2015, 48(3): 407-414.

[21] 张玲, 郭爽, 汪玲, 张天泉, 庄慧, 龙珏臣等. 水稻矮化并花发育异常突变体dwarf and deformed flower 2(ddf2)的基因定位与候选基因分析. 中国农业科学, 2015, 48(10): 1873-1881.

ZAHNG L, GUO S, WANG L, ZHANG T Q, ZHAUNG H, LONG Y C. Gene mapping and candidate gene analysis of a dwarf and deformed flower 2 (ddf2) mutant in rice (Oryza sativa). Scientia Agricultura Sinica, 2015, 48(10): 1873-1881.

[22] 苗晗, 顾兴芳, 张圣平, 张忠华, 黄三文, 王烨. 利用永久群体在不同环境下定位黄瓜株高QTL. 中国农业科学, 2012, 45(22): 4552-4560.

MIAO H, GU X F, ZHANG S P, ZHANG Z H, HAUNG S W, WANG Y. Detection of quantitative trait loci for plant height in different environments using an RIL population in cucumber. Scientia Agricultura Sinica, 2012, 45(22): 4552-4560.

[23] LODHI M A, YE G N, WEEDEN N F, REISCH B I. A simple and efficient method for DNA extraction from grapevine cultivars and Vitis species. Plant Molecular Biology Reporter, 1994, 12(1): 6-13.

[24] VAN OOIJEN J W. JoinMap 4: Software for the calculation of genetic linkage maps in experimental populations.Kyazma BV, Wageningen, Netherlands. 2006.

[25] VAN OOIJEN J W. MapQTL® 5. Software for the mapping of quantitative trait loci in experimental populations.Kyazma BV, Wageningen, Netherlands. 2004.

[26] WANG Z, WEBER J L, ZHONG G, TANKSLEY S D. Survey of plant short tandem DNA repeats. Theoretical and Applied Genetics, 1994, 88(1): 1-6.

[27] LEVINSON G, GUTMAN G A. Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Molecular Biology And Evolution, 1987, 4(3): 203-221.

[28] RICHARDS R I, SUTHERLAND G R. Dynamic mutations: a new class of mutations causing human disease. Cell, 1992, 70(5): 709-712.

[29] LIEBHARD R, KOLLER B, GIANFRANCESCHI L, GESSLER C. Creating a saturated reference map for the apple (Malus × domestica Borkh.) genome. Theoretical & Applied Genetics, 2003, 106(8): 1497-1508.

[30] KENIS K, KEULEMANS J, DAVEY M W. Identification and stability of QTLs for fruit quality traits in apple. Tree Genetics & Genomes,2008, 4(4): 647-661.