High Density Genetic Map of Cultivated Strawberry by SLAF-seq

doi:10.7668/hbnxb.20191341

Abstract

Abstract: For the development of a large number of SNP for the construction of high quality genetic map of cultivated strawberry(Fragaria×ananassa,2n=8X=56),Hongxing×Benihoppe crossing populations were sequenced by SLAF-seq that yielded 565 919 066 reads, with Q30 value of 95.36% and GC content of 39.68%. 717 881 SLAFs and 2 136 939 SNPs were identified.Total 56 237 SNPs showed high quality for genetic map construction, of which 14 412 were successfully mapped to 28 linkage groups spanning a total of 4 022.16 cM with an average interval genetic distance of 0.28 cM. It was showed that the greater part of each individual was derived from the parents by evaluating the monomer source of the genetic map. The results of heat map showed that the sequence of most markers on each linkage group was consistent with the genome, the sequence of markers was correct, which could show that the map was of high quality.A high-density genetic map of cultivated strawberry by SLAF-seq could be laying a foundation for genetic research and molecular marker-assisted breeding of cultivated strawberry.

Key words: Cultivated strawberry, SLAF-seq, SNP, High density genetic map

CLC Number:

S668.03

DONG Hui, YANG Li, LI Li, ZHANG Jianjun, FAN Jingfang, SONG Shijia, YANG Lei, LI Haishan. High Density Genetic Map of Cultivated Strawberry by SLAF-seq[J]. ACTA AGRICULTURAE BOREALI-SINICA, 2020, 35(6): 52-57. doi: 10.7668/hbnxb.20191341.

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References

[1] 赵密珍, 王静, 袁华招, 王庆莲,关玲.草莓育种新动态及发展趋势[J].植物遗传资源学报, 2019, 20(2):249-257.doi:10.13430/j.cnki.jpgr.20181102001.
Zhao M Z,Wang J,Yuan H Z,Wang Q L,Guan L.Situation and perspectives of strawberry breeding[J]. Journal of Plant Genetic Resources,2019, 20(2):249-257.
[2] Staudt G. Taxonomic studies in the genus Fragaria typification of Fragaria species known at the time of linnaeus[J]. Canadian Journal of Botany, 1962,40(6):869-886.doi:10.1139/b62-081.
[3] Sargent D J, Fernandéz-Fernandéz F, Ruiz-Roja J J, Sutherland B G, Passey A, Whitehouse A B, Simpson D W. A genetic linkage map of the cultivated strawberry(Fragaria×ananassa) and its comparison to the diploid Fragaria reference map[J]. Molecular Breeding,2009,24(3):293-303.doi:10.1007/s11032-009-9292-9.
[4] Sargent D J, Passey T, Šurbanovski N, Girona E L, Kuchta P, Davik J, Harrison R, Passey A, Whitehouse A B, Simpson D W.A microsatellite linkage map for the cultivated strawberry(Fragaria×ananassa) suggests extensive regions of homozygosity in the genome that may have resulted from breeding and selection[J]. Theoretical and Applied Genetics, 2012, 124(7):1229-1240.doi:10.1007/s00122-011-1782-6.
[5] Isobe S N, Hirakawa H, Sato S, Maeda F, Ishikawa M, Mori T, Yamamoto Y, Shirasawa K, Kimura M, Fukami M, Hashizume F, Tsuji T, Sasamoto S, Kato M, Nanri K, Tsuruoka H, Minami C, Takahashi C, Wada T, Ono A, Kawashima K, Nakazaki N, Kishida Y, Kohara M, Nakayama S, Yamada M, Fujishiro T, Watanabe A, Tabata S. Construction of an integrated high density simple sequence repeat linkage map in cultivated strawberry(Fragaria ananassa) and its applicability[J]. DNA Research, 2013,20(1):79-92.doi:10.1093/dnares/dss035.
[6] Weebadde C K, Wang D, Finn C E, Lewers K S, Luby J J, Bushakra J, Sjulin T M, Hancock J F. Using a linkage mapping approach to identify QTL for day-neutrality in the octoploid strawberry[J]. Plant Breeding,2008,127(1):94-101.doi:10.1111/j.1439-0523.2007.01430.x.
[7] van Dijk T, Pagliarani G, Pikunova A, Noordijk Y, Yilmaz-Temel H, Meulenbroek B, Visser R G, van de Weg E.Genomic rearrangements and signatures of breeding in the allo-octoploid strawberry as revealed through an allele dose based SSR linkage map[J]. BMC Plant Biology, 2014,14(1):55.doi:10.1186/1471-2229-14-55.
[8] Castro P, Bushakra J M, Stewart P, Weebadde C K, Wang D, Hancock J F, Finn C E, Luby J J, Lewers K S. Genetic mapping of day-neutrality in cultivated strawberry[J]. Molecular Breeding,2015, 35(2):79.doi:10.1007/s11032-015-0250-4.
[9] Bassil N V, Davis T M, Zhang H L, Ficklin S,Mittmann M,Webster T,Mahoney L,Wood D, Alperin E S,Rosyara U R, Putten H K,Monfort A, Sargent D J, Amaya I,Denoyes B, Bianco L, Van Dijk T,Pirani A,Iezzoni A, Main D, Peace C, Yang Y L, Whitaker V, Verma S,Bellon L, Brew F,Herrera R, Weg E.Development and preliminary evaluation of a 90 K Axiom^® SNP array for the allo-octoploid cultivated strawberry Fragaria ananassa[J]. BMC Genomics, 2015,16(1):155.doi:10.1186/s12864-015-1310-1.
[10] Nagano S, Shirasawa K, Hirakawa H,Maeda F,Ishikawa M,Isobe S N.Discrimination of candidate subgenome-specific loci by linkage map construction with an S₁ population of octoploid strawberry(Fragaria×ananassa)[J]. BMC Genomics, 2017,18(1):374.doi:10.1186/s12864-017-3762-y.
[11] 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.
[12] Huang X H, Zhao Y, We X H, Li C Y, Wang A H, Zhao Q, Li W J, Guo Y L, Deng L W, Zhu C R, Fan D L, Lu Y Q, Weng Q J, Liu K Y, Zhou T Y, Jing Y F, Si L Z, Dong G J, Huang T, Lu T T, Feng Q, Qian Q, Li J Y, Han B. Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm[J]. Nature Genetics, 2012, 44(1):32-39.doi:10.1038/ng.1018.
[13] Stam P. Construction of integrated genetic linkage maps by means of a new computer package:JOIN MAP[J]. The Plant Journal, 1993,3(5):739-744.doi:10.1111/j.1365-313X.1993.00739.x.
[14] Liu D Y, Ma C X, Hong W G, Huang L, Liu M, Liu H, Zeng H P, Deng D J, Xin H G,Song J, Xu C H,Sun X W,Hou X L,Wang X W, Zheng H K. Construction and analysis of high-density linkage map using high-throughput sequencing data[J]. PLoS One,2014, 9(6):e98855.doi:10.1371/journal.pone.0098855.
[15] Sun X W, Liu D Y, Zhang X F, Li W B, Liu H, Hong W G, Jiang C B,Guan N,Ma C X,Zeng H P,Xu C H,Song J,Huang L,Wang C M,Shi J J,Wang R,Zheng X H,Lu C Y,Wang X W, Zheng H K.SLAF-seq:an efficient method of large-scale de novo SNP discovery and genotyping using high-throughput sequencing[J]. PLoS One, 2013,8(3):e58700.doi:10.1371/journal.pone.0058700.
[16] Delourme R, Falentin C, Fomeju B F, Boillot M, Lassalle G, André I, Duarte J, Gauthier V, Lucante N, Marty A, Pauchon M, Pichon J P, Ribière N, Trotoux G, Blanchard P, Rivière N, Martinant J P, Pauquet J.High-density SNP-based genetic map development and linkage disequilibrium assessment in Brassica napus L.[J]. BMC Genomics, 2013, 14(1):120.doi:10.1186/1471-2164-14-120.
[17] Moreno R, Castro P, Vrána J, Kubaláková M, Cápal P, García V, Gil J, Millán T, Doležel J.Integration of genetic and cytogenetic maps and identification of sex chromosome in garden Asparagus(Asparagus officinalis L.)[J]. Frontiers in Plant Science, 2018, 9:1068.doi:10.3389/fpls.2018.01068.
[18] Garg T, Mallikarjuna B P, Thudi M, Samineni S, Singh S, Sandhu J S,Kaur L, Singh I,Sirari A,Basandrai A K,Basandrai D,Varshney R K,Gaur P M. Identification of QTLs for resistance to Fusarium wilt and Ascochyta blight in a recombinant inbred population of chickpea(Cicer arietinum L.)[J]. Euphytica, 2018, 214(3):45.doi:10.1007/s10681-018-2125-3.
[19] 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 ence, 2014, 5(768):768.doi:10.3389/fpls.2014.00768.
[20] Gong D P, Huang L, Xu X H, Wang C Y,Ren M, Wang C K,Chen M L. Construction of a high-density SNP genetic map in flue-cured tobacco based on SLAF-seq[J]. Molecular Breeding, 2016, 36(7):100.doi:10.1007/s11032-016-0514-7.
[21] 高凤云,斯钦巴特尔,张辉,贾霄云,伊六喜,周宇,李强,叶应福,侯建华.基于SLAF-seq技术构建亚麻高密度遗传图谱[J].中国油料作物学报, 2017, 39(3):334-341.doi:10.7505/j.issn.1007-9084.2017.03.007.
Gao F Y,Si Q B T,Zhang H,Jia X Y,Yi L X,Zhou Y,Li Q,Ye Y F,Hou J H. High density genetic map of flax based on SLAF-seq technology[J]. Chinese Journal of Oil Crop Sciences, 2017, 39(3):334-341.
[22] Wang L, Li X G, Wang L,Xue H B,Wu J,Yin H,Zhang S L. Construction of a high-density genetic linkage map in pear(Pyrus communis×Pyrus pyrifolia nakai) using SSRs and SNPs developed by SLAF-seq[J]. Scientia Horticulturae, 2017, 218:198-204.doi:10.1016/j.scienta.2017.02.015.
[23] 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 C H, Chen D M,Yang F Q,Zhao T S,Li Y, Zhao G D, Zhao Y B.Genetic mapping and QTL analysis of fruit russeting in Malus domestica Borkh[J]. Acta Agriculturae Boreali-Sinica, 2019, 34(5):37-44.
[24] Davik J, Sargent D J, Brurberg M B, Lien S,Kent M,Alsheikh M. A ddRAD based linkage map of the cultivated strawberry, Fragaria ananassa[J]. PLoS One, 2015,10(9):e137746.doi:10.1371/journal.pone.0137746.
[25] Lee Y R,Lee J. A genetic linkage map of allo-octoploid strawberry(Fragaria×ananassa Duch.) using SNP markers[J]. Korean Journal of Breeding Science,2017,49(3):119-128.doi:10.9787/KJBS.2017.49.3.119.
[26] Hossain M R, Natarajan S, Kim H T, Jesse D M I, Lee C G, Park J,Nou I S. High density linkage map construction and QTL mapping for runner production in allo-octoploid strawberry Fragaria×ananassa based on ddRAD-seq derived SNPs[J]. Scientific Reports, 2019,9(1):3275.doi:10.1038/s41598-019-39808-9.

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