苹果SLAF图谱构建及果锈基因QTL分析

doi:10.7668/hbnxb.201751695

摘要/Abstract

摘要： 为了定位苹果果锈的QTL，鉴定果锈基因的遗传位点，以解析苹果果锈基因的分子遗传基础。以宫崎短枝富士×坂田津轻分离群体及其亲本为材料，基于SLAF-seq技术开发分子标签，并构建高密度遗传图谱，结合3个年份的田间表型数据，采用mapqtl进行果锈基因的QTL分析。结果表明，获得了522 122 315 reads（110.32 Gb）的测序数据，测序平均Q30为95.07%，平均GC含量为40.11%；开发了20 440个SLAF标签，7 309 729个SNP；构建了17个连锁群，4 075个上图标记，总图距为2 235.23 cM，平均图距达0.55 cM，上图标记的完整度为99.92%。共检测到了9个果锈相关的QTL，分别分布在Chr3、Chr9、Chr11、Chr15染色体上，标记距离为0~4.9 cM，贡献率为18.0%~85.5%。其中，检测到控制果锈的Qru-9、Qru-15、Qru-3的贡献率较高，可能是控制苹果果锈的关键位点。构建了苹果SLAF遗传图谱，获得了9个与果锈相关的QTL，研究结果对于苹果果锈及其相关基因的进一步挖掘与利用具有重要意义。

关键词: 苹果, 果锈, SLAF, 遗传图谱, QTL分析

Abstract: In order to effectively discover the apple fruit russet gene, based on SLAF-seq technology, the genetic map construction and QTL analysis for fruit russet gene were conducted using a population derived from a cross between Miyazaki Spur and Sakata Tsugaru. The results showed that 522 122 315 reads (110.32 Gb) of the sequencing data from seedlings was obtained, in which the average Q30 sequencing was 95.07%, and the average GC content and its parents was 40.11%. Then, 20 440 SLAF markers and 7 309 729 SNPs were developed. Based on these markers, seventeen linkage groups were constructed, of which 4 075 markers presented in the genetic map, and marker integrity was 99.92%. The total diagram spacing was 2 235.23 cM, and the average diagram spacing was 0.55 cM. A total of 9 QTLs related to fruit russet were detected, which were distributed on Chr3, Chr9, Chr11, and Chr15 chromosomes, with a marker distance of 0-4.9 cM and a contribution rate of 18.0%-85.5%. Among them, Qru-9, Qru-15 and Qru-3, located on Chromosome 9, 3, and 15, respectively, might be novel QTLs for fruit russeting of apple. A genetic map based on SLAF-seq method was constructed in apple progeny Miyazaki Spur crossing Sakata Tsugaru and nine QTLs related to apple russeting were obtained. These results provided the important information for further exploration of russeting QTL in apple.

中图分类号:

S661.03

张朝红, 陈东玫, 杨凤秋, 赵同生, 李扬, 赵国栋, 赵永波. 苹果SLAF图谱构建及果锈基因QTL分析[J]. 华北农学报, 2019, 34(5): 37-44. doi: 10.7668/hbnxb.201751695.

ZHANG Chaohong, CHEN Dongmei, YANG Fengqiu, ZHAO Tongsheng, LI Yang, ZHAO Guodong, ZHAO Yongbo. Genetic Mapping and QTL Analysis of Fruit Russeting in Malus domestica Borkh.[J]. ACTA AGRICULTURAE BOREALI-SINICA, 2019, 34(5): 37-44. doi: 10.7668/hbnxb.201751695.

http://www.hbnxb.net/CN/Y2019/V34/I5/37

参考文献

[1] Andre C M, Larsen L, Burgess E J,Jensen D J,Cooney J M,Evers D,Zhang J L,Perry N B,Laing W A.Unusual immuno-modulatory triterpene-caffeates in the skins of russeted varieties of apples and pears[J].Journal of Agricultural and Food Chemistry,2013,61(11):2773-2779. doi:10.1021/jf305190e.
[2] Wang Y Z, Dai M S, Zhang S J, Shi Z B.Exploring candidate genes for pericarp russet pigmentation of sand pear(Pyrus pyrifolia)via RNA-Seq data in two genotypes contrasting for pericarp color[J].PLoS One,2014,9(1):e83675. doi:10.1371/journal.pone.0083675.
[3] Hou X D, Wei L L, Xu Y S,Khalil-Ur-Rehman M,Feng J,Zeng J J,Tao J M.Study on russet-related enzymatic activity and gene expression in ‘shine Muscat’ grape treated with GA3 and CPPU[J].Journal of Plant Interaction,2017,13(1):195-202.doi:10.1080/17429145.2018.1455904.
[4] Bethke P C, Nassar A M K, Kubow S, Leclerc Y N, Li X Q, Haroon M, Molen T,Bamberg J, Martin M, Donnelly D J. History and origin of russet burbank (Netted Gem) a sport of Burbank[J]. American Journal of Potato Research, 2014, 91(6):594-609. doi:10.1007/s12230-014-9397-5.
[5] Massa A N, Manrique-Carpintero N C, Coombs J, Haynes K G, Bethke P C, Brandt T L, Cupta S K, Yencho G C, Novy R G, Douches D S.Linkage analysis and QTL mapping in a tetraploid russet mapping population of potato[J].BMC Genetics,2018,19(1):87.doi:10.1186/s12863-018-0672-1.
[6] Thangavel T, Tegg R S, Wilson C R.Resistance to multiple tuber diseases expressed in somaclonal variants of the potato cultivar russet burbank[J].The Scientific World Journal,2014:417697.doi:10.1155/2014/417697.
[7] 宋伟, 王彩虹, 田义轲, 田伟, 殷豪. 梨果实褐皮性状的SSR标记[J]. 园艺学报, 2010, 37(8):1325-1328.
Sng W, Wang C H, Tian Y K, Tian W, Yan H. SSR molecular markers linked to the fruit russet skin of pear[J]. Acta Horticulturae Sinica, 2010,37(8):1325-1328.
[8] 吴厚玖, 陈荣柱, 李育农. 金冠苹果果锈发生时期与锈化过程的研究[J]. 园艺学报, 1984, 11(1):51-54.
W H J, Chen Y Z, Li Y N. Studies on the date of occurrence and histological development of russeting in Golden delicious apples[J]. Acta Horticulturae Sinica, 1984, 11(1):51-54.
[9] 夏春森, 周萍. 影响‘金冠’苹果果锈形成的因子[J]. 园艺学报, 1988, 15(2):139-142.
Xan C S, Zhou P. Factors influencing the formation of russet on the fruit of ‘Golden Delicious’ apple[J]. Acta Horticulturae Sinica, 1988, 15(2):139-142.
[10] Gildemacher P R, Heijne B, Houbraken J, Vromans T, Hoekstra E S, Boekhout T.Can phyllosphere yeasts explain the effect of scab fungicides on russeting of Elstar apples?[J].European Journal of Plant Pathology,2004,110(9):929-937.doi:10.1007/S10658-004-8948-x.
[11] Legay S, Guerriero G, Deleruelle A, Lateur M, Evers D, Andre C M, Hausman J F.Apple russeting as seen through the RNA-seq lens:strong alterations in the exocarp cell wall[J].Plant Molecular Biology,2015,88(1-2):21-40.doi:10.1007/s11103-015-0303-4.
[12] Bell H P.The origin of russeting in the Golden russet apple[J].Canadian Journal of Research,1937,15c(12):560-566. doi:10.1139/cjr37c-042.
[13] Verner L.Histology of apple fruit tissue in relation to cracking[J].Journal of Agricultural Research,1938,57(11):813-824.
[14] Noè N, Eccher T. ‘Golden Delicious’ apple fruit shape and russeting are affected by light conditions[J]. Scientia Horticulturae, 1996, 65(2-3):209-213. doi:10.1016/0304-4238(95)00850-0.
[15] Dillard H R, Cobb A C, Shah D A, Straight K E.Identification and characterization of russet on snap beans caused by Plectosporium tabacinum[J].Plant Disease,2005,89(7):700-704.doi:10.1094/PD-89-0700.
[16] Gildemacher P, Heijne B, Silvestri M, Hoekstra J, Hoekstra E, Theelen B, Boekhout T.Interactions between yeasts, fungicides and apple fruit russeting[J].FEMS Yeast Research,2006,6(8):1149-1156.doi:10.1111/j.1567-1364.2006.00109.x.
[17] 李健花,高晶晶,冯新新, 师忠轩, 高付永, 徐秀丽, 杨丽媛, 汪良驹. ‘金冠’苹果与其无锈芽变的果皮性状比较和防锈技术研究[J]. 园艺学报, 2014, 41(1):35-43.doi:10.3969/j.issn.0513-353x.2014.01.005.
L J H, Gao J J, Feng X X, Shi Z X, Gao F Y, Xu X L, Yang L Y, Wang L J. Comparison of peel characteristics between ‘Golden Delicious’ and its Non-russet sport ‘Fengshuai’ apples to explore a method to prevent fruit russeting[J]. Acta Horticulturae Sinica, 2014, 41(1):35-43.
[18] Heng W, Wang M D, Yang J Y, Wang Z T, Jiang X H, Zhu L W.Relationship between H₂O₂ in polyamine metabolism and lignin in the exocarp of a russet mutant of ‘Dangshansuli’ Pear (Pyrus bretschneideri Rehd.)[J].Plant Molecular Biology Reporter,2016,34(6):1056-1063.doi:10.1007/s11105-016-0985-z.
[19] Heng W, Wang Z T, Jiang X H, Jia B, Liu P, Liu L, Ye Z F, Zhu L W.The role of polyamines during exocarp formation in a russet mutant of ‘Dangshansuli’ pear (Pyrus bretschneideri Rehd.)[J].Plant Cell Reports,2016,35(9):1841-1852.doi:10.1007/s00299-016-1998-7.
[20] Wang Y Z, Dai M S, Cai D Y, Zhang S A, Shi Z B.A review for the molecular research of russet/semi-russet of sand pear exocarp and their genetic characters[J].Scientia Horticulturae,2016,210:138-142.doi:10.1016/j.scienta.2016.07.019.
[21] Legay S, Guerriero G, André C, Guignard C, Cocco E, Charton S, Boutry M,Rowland O,Hausman J F.MdMyb93 is a regulator of suberin deposition in russeted apple fruit skins[J].New Phytologist,2016,212(4):977-991. doi:10.1111/nph.14170.
[22] Hou Z Q, Jia B, Li F, Liu P, Liu L, Ye Z F, Zhu L W, Wang Q, Heng W. Characterization and expression of the ABC family (G group) in ‘Dangshansuli’ pear (Pyrus bretschneideri Rehd.) and its russet mutant[J].Genetics and Molecular Biology,2018,41(1):137-144. doi:10.1590/1678-4685-gmb-2017-0109.
[23] Durel C E, Laurens F, Fouillet A, Lespinasse Y.Utilization of pedigree information to estimate genetic parameters from large unbalanced data sets in apple[J].Theoretical and Applied Genetics,1998,96(8):1077-1085.doi:10.1007/s001220050842.
[24] 刘志, 伊凯, 王冬梅, 杨巍, 杨锋, 张景娥. 富士苹果果实外观品质性状的遗传[J]. 果树学报, 2004, 21(6):505-511.doi:10.3969/j.issn.1009-9980.2004.06.001.
Lu Z, Yi K, Wang D M, Yang W, Yang F, Zhang J E. Study on the inheritance of external characteristics of Fuji apple fruit[J]. Journal of Fruit Science, 2004,21(6):505-511.
[25] Falginella L, Cipriani G, Monte C, Gregori R, Testolin R, Velasco R, Troggio M, Tartarini S.A major QTL controlling apple skin russeting maps on the linkage group 12 of ‘Renetta Grigia di Torriana’[J].BMC Plant Biology, 2015,15:150.doi:10.1186/s12870-015-0507-04.
[26] Kozich J J, Westcott S L, Baxter N T, Highlander S K, Schloss P D.Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq illumina sequencing platform[J].Applied and Environmental Microbiology,2013,79(17):5112-5120.doi:10.1128/AEM.01043-13.
[27] Stam P.Construction of integrated genetic linkage maps by means of a new computer package:JoinMap[J].The Plant Journal,1993,3(5):739-744. doi:10.1111/j.1365-313x.1993.00739.x.
[28] Li R Q, Li Y R, Kristiansen K, Wang J.SOAP:short oligonucleotide alignment program[J].Bioinformatics,2008,24(5):713-714.doi:10.1093/bioinformatics/btn025.
[29] Xu X W, Xu R X, Zhu B Y, Yu T, Qu W Q, Lu L, Xu Q, Qi X H, Chen X H. A high-density genetic map of cucumber derived from specific length amplified fragment sequencing (SLAF-seq)[J]. Frontiers in Plant Science, 2014, 5:768. doi:10.3389/fpls.2014.00768.
[30] Guo Y S, Shi G L, Liu Z D, Zhao Y H, Yang X X, Zhu J C, Li K, Guo X W.Using specific length amplified fragment sequencing to construct the high-density genetic map for Vitis (Vitis vinifera L. ×Vitis amurensis Rupr.)[J].Frontiers in Plant Science,2015,6:393.doi:10.3389/fpls.2015.00393.
[31] 俞奔驰, 韦丽君, 雷开文, 宋恩亮, 马崇熙. 基于SLAF-seq技术的木薯SNP标记开发[J]. 植物生理学报, 2018, 54(6):1029-1037. doi:10.13592/j.cnki.ppj.2018.0029.
Y B C, Wei L J, Lei K W, Song E L, Ma C X. Development of SNP markers in cassava (Manihot esculenta Crantz) based on SLAF-seq technology[J]. Plant Physiology Journal, 2018, 54(6):1029-1037.
[32] Lu J J, Liu Y Y, Xu J, Mei Z W, Shi Y J, Liu P L, He J B, Wang X T, Meng Y J, Feng S G, Shen C J, Wang H Z. High-density genetic map construction and stem total polysaccharide content-related QTL exploration for Chinese Endemic Dendrobium (Orchidaceae)[J]. Frontier in Plant Science, 2018,9:398. doi:10.3389/fpls.2018.00398.
[33] Xia C, Chen L L, Rong T Z, Li R, Xiang Y, Wang P, Liu C H, Dong X Q, Liu B, Zhao D, Wei R J, Lan H.Identification of a new maize inflorescence meristem mutant and association analysis using SLAF-seq method[J].Euphytica,2015,202(1):35-44.doi:10.1007/s10681-014-1202-5.
[34] 杜龙岗,王美兴. 玉米SLAF标记的开发及其在玉米果皮纤维素含量BSA分析中的应用[J]. 中国农业科学, 2018, 51(8):1421-1430. doi:10.3864/j.issn.0578-1752.2018.08.001.
D L G, Wang M X. SLAF-marker development and its application in BSA analysis of cellulose content in pericarp of maize kernel[J]. Scientia Agricultura Sinica, 2018, 51(8):1421-1430.
[35] Kumar S, Bink M C A M, Volz R K, Bus V G M, Chagné D.Towards genomic selection in apple (Malus domestica Borkh.) breeding programmes:Prospects, challenges and strategies[J].Tree Genetics & Genomes,2012,8(1):1-14.doi:10.1007/s11295-011-0425-z.

选择文件类型/文献管理软件名称

选择包含的内容