Special Issue:
油料作物合辑Oil Crops
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QTL analysis for plant height and fine mapping of two environmentally stable QTLs with major effects in soybean |
TIAN Yu1, YANG Lei1, LU Hong-feng2, ZHANG Bo3, LI Yan-fei1, LIU Chen1, 4, GE Tian-li1, LIU Yu-lin5, HAN Jia-nan1, LI Ying-hui1, QIU Li-juan1 |
1 National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture and Rural Affairs/Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing 100081, P.R.China
2 Novogene Bioinformatics Institute, Beijing 100015, P.R.China
3 School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24060, USA
4 School of Life Sciences, Liaoning Normal University, Dalian 116081, P.R.China
5 College of Forestry, Northwest A&F University, Yangling 712100, P.R.China
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摘要
大豆株高是由主效或微效基因控制的重要农艺性状。在已报道的株高QTL中,绝大部分定位区间较大,限制了大豆株高分子调控机制的解析。增加遗传图谱的标记密度会显著地提高QTL定位的效率和准确性。本研究利用双亲中黄13和中品03-5373及其衍生的241个重组自交系(RILs)全基因组重测序数据,构建一个包含4011个重组bin标记、总遗传距离为3139.15 cM的高密度遗传图谱,相邻bin标记间的平均距离为0.78 cM。比较基因组分析表明,所构建的遗传图谱与大豆参考基因组具有较高的共线性。基于此图谱,在6个环境中共检测到9个株高QTL,包括3个新位点(qPH-b_11,qPH-b_17和qPH-b_18)。其中,两个环境稳定主效QTL qPH-b_13和qPH-b_19-1可解释10.56%~32.7%的表型变异。qPH-b_13和qPH-b_19-1被精细定位到440.12 kb和237.06 kb的基因组区间,分别包含54和28个注释基因。进一步的拟南芥同源基因功能和候选基因表达分析表明,基因Glyma.13G292600和Glyma.19G194100分别为qPH-b_13和qPH-b_19-1的候选功能基因。
Abstract Plant height is an important agronomic trait, which is governed by multiple genes with major or minor effects. Of numerous QTLs for plant height reported in soybean, most are in large genomic regions, which results in a still unknown molecular mechanism for plant height. Increasing the density of molecular markers in genetic maps will significantly improve the efficiency and accuracy of QTL mapping. This study constructed a high-density genetic map using 4 011 recombination bin markers developed from whole genome re-sequencing of 241 recombinant inbred lines (RILs) and their bi-parents, Zhonghuang 13 (ZH) and Zhongpin 03-5373 (ZP). The total genetic distance of this bin map was 3 139.15 cM, with an average interval of 0.78 cM between adjacent bin markers. Comparative genomic analysis indicated that this genetic map showed a high collinearity with the soybean reference genome. Based on this bin map, nine QTLs for plant height were detected across six environments, including three novel loci (qPH-b_11, qPH-b_17 and qPH-b_18). Of them, two environmentally stable QTLs qPH-b_13 and qPH-b_19-1 played a major role in plant height, which explained 10.56–32.7% of the phenotypic variance. They were fine-mapped to 440.12 and 237.06 kb region, covering 54 and 28 annotated genes, respectively. Via the function of homologous genes in Arabidopsis and expression analysis, two genes of them were preferentially predicted as candidate genes for further study.
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Received: 06 July 2020
Accepted: 25 March 2021
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Fund: This research was supported by the National Key R&D Program of China (2016YFD0100201) and the Agricultural Science and Technology Innovation Program (ASTIP) of Chinese Academy of Agricultural Sciences. |
About author: TIAN Yu, E-mail: 82101181082@caas.cn; Correspondence LI Ying-hui Tel: +86-10-82105843, Fax: +86-10-82105840, E-mail: liyinghui@caas.cn; QIU Li-juan, E-mail: qiulijuan@caas.cn |
Cite this article:
TIAN Yu, YANG Lei, LU Hong-feng, ZHANG Bo, LI Yan-fei, LIU Chen, GE Tian-li, LIU Yu-lin, HAN Jia-nan, LI Ying-hui, QIU Li-juan.
2022.
QTL analysis for plant height and fine mapping of two environmentally stable QTLs with major effects in soybean. Journal of Integrative Agriculture, 21(4): 933-946.
|
Baumbach J, Rogers J P, Slattery R A, Narayanan N N, Xu M, Palmer R G, Bhattacharyya M K, Sandhu D. 2012. Segregation distortion in a region containing a male-sterility, female-sterility locus in soybean. Plant Science, 195, 151–156.
Bischoff V, Nita S, Neumetzler L, Schindelasch D, Urbain A, Eshed R, Persson S, Delmer D, Scheible W R. 2010. Trichome birefringence and its homolog AT5G01360 encode plant-specific DUF231 proteins required for cellulose biosynthesis in Arabidopsis. Plant Physiology, 153, 590–602.
Cai Z D, Cheng Y B, Ma Z W, Liu X G, Ma Q B, Xia Q J, Zhang G Y, Mu Y H, Nian H. 2018. Fine-mapping of QTLs for individual and total isoflavone content in soybean (Glycine max L.) using a high-density genetic map. Theoretical and Applied Genetics, 131, 555–568.
Chapman A, Pantalone V R, Ustun A, Allen F L, Landau-Ellis D, Trigiano R N, Gresshoff P M. 2003. Quantitative trait loci for agronomic and seed quality traits in an F2 and F4:6 soybean population. Euphytica, 129, 387–393.
Chen Z L, Wang B B, Dong X M, Liu H, Ren L H, Chen J, Hauck A, Song W B, Lai J S. 2014. An ultra-high density bin-map for rapid QTL mapping for tassel and ear architecture in a large F2 maize population. BMC Genomics, 15, 433.
Davière J M, Wild M, Regnault T, Baumberger N, Eisler H, Genschik P, Achard P. 2014. Class I TCP-DELLA interactions in inflorescence shoot apex determine plant height. Current Biology, 24, 1923–1928.
Doyle J J, Doyle J L. 1990. Isolation of plant DNA from fresh tissue. Focus, 12, 39–40.
Elshire R J, Glaubitz J C, Sun Q, Poland J A, Kawamoto K, Buckler E S, Mitchell S E. 2011. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE, 6, e19379.
Fang C, Ma Y M, Wu S W, Liu Z, Wang Z, Yang R, Hu G H, Zhou Z K, Yu H, Zhang M, Pan Y, Zhou G A, Ren H X, Du W G, Yan H R, Wang Y P, Han D Z, Shen Y T, Liu S L, Liu T F, et al. 2017. Genome-wide association studies dissect the genetic networks underlying agronomical traits in soybean. Genome Biology, 18, 161.
Henderson C R. 1975. Best linear unbiased estimation and prediction under a selection model. Biometrics, 31, 423–447.
Huang X H, Feng Q, Qian Q, Zhao Q A, Wang L, Wang A, Guan J P, Fan D L, Weng Q J, Huang T. 2009. High-throughput genotyping by whole-genome resequencing. Genome Research, 19, 1068.
Ji F Y, Wei W, Liu Y, Wang G P, Zhang Q, Xing Y, Zhang S H, Liu Z H, Cao Q Q, Qin L. 2018. Construction of a SNP-based high-density genetic map using genotyping by sequencing (GBS) and QTL analysis of nut traits in Chinese chestnut (Castanea mollissima Blume). Frontiers in Plant Science, 9, 816.
Josie J, Kassem M A. 2007. Genomic regions containing QTL for plant height, internodes length, and flower color in soybean [Glycine max (L.) Merr.]. Bios, 78, 119–126.
Kim K S, Diers B W, Hyten D L, Mian M A R, Shannon J G, Nelson R L. 2012. Identification of positive yield QTL alleles from exotic soybean germplasm in two backcross populations. Theoretical and Applied Genetics, 125, 1353–1369.
Kim Y S, Kim S G, Lee M, Lee I, Park H Y, Seo P J, Jung J H, Kwon E J, Suh S W, Paek K H. 2008. HD-ZIP III activity is modulated by competitive inhibitors via a feedback loop in Arabidopsis shoot apical meristem development. The Plant Cell, 20, 920–933.
Lee S, Jun T H, Michel A P, Mian M A R. 2015. SNP markers linked to QTL conditioning plant height, lodging, and maturity in soybean. Euphytica, 203, 521–532.
Lee S H, Bailey M A, Mian M, Shipe E R, Ashley D A, Parrott W A, Hussey R S, Boerma H R. 1996. Identification of quantitative trait loci for plant height, lodging, and maturity in a soybean population segregating for growth habit. Theoretical and Applied Genetics, 92, 516–523.
Li B, Fan S X, Yu F K, Chen Y, Zhang S R, Han F X, Yan S R, Wang L Z, Sun J M. 2017. High-resolution mapping of QTL for fatty acid composition in soybean using specific-locus amplified fragment sequencing. Theoretical and Applied Genetics, 130, 1467–1479.
Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754–1760.
Li H, Kilian A, Zhou M, Wenzl P, Huttner E, Mendham N, McIntyre L, Vaillancourt R E. 2010. Construction of a high-density composite map and comparative mapping of segregation distortion regions in barley. Molecular Genetics and Genomics, 284, 319–331.
Li H B, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. 2009a. The sequence alignment/map format and SAMtools. Bioinformatics, 25, 2078–2079
Li H B, Zhou M X, Liu C J. 2009b. A major QTL conferring crown rot resistance in barley and its association with plant height. Theoretical and Applied Genetics, 118, 903–910.
Li H H, Ribaut J M, Li Z L, Wang J K. 2008. Inclusive composite interval mapping (ICIM) for digenic epistasis of quantitative traits in biparental populations. Theoretical and Applied Genetics, 116, 243–260.
Li Y H, Liu B, Reif J C, Liu Y L, Li H H, Chang R Z, Qiu L J. 2014. Development of insertion and deletion markers based on biparental resequencing for fine mapping seed weight in soybean. Plant Genome, 7, 1–8.
Li Y H, Zhao S C, Ma J X, Li D, Yan L, Li J, Qi X T, Guo X S, Zhang L, He W M, Chang R Z, Liang Q S, Guo Y, Ye C, Wang X B, Tao Y, Guan R X, Wang J Y, Liu Y L, Jin L G, et al. 2013. Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing. BMC Genomics, 14, 579.
Liu H J, Niu Y C, Gonzalez-Portilla P J, Zhou H K, Wang L Y, Zuo T, Qin C, Tai S S, Jansen C, Shen Y O, Lin H J, Lee M, Ware D, Zhang Z M, Luebberstedt T, Pan G T. 2015. An ultra-high-density map as a community resource for discerning the genetic basis of quantitative traits in maize. BMC Genomics, 16, 1078.
Liu Y L, Li Y, Reif J C, Mette M F, Liu Z X, Liu B, Zhang S S, Yan L, Chang R Z, Qiu L J. 2013. Identification of quantitative trait loci underlying plant height and seed weight in soybean. Plant Genome, 6, 1–11.
Livak K J, Schmittgen T D. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2–∆∆CT. Method, 25, 402–408.
Lu H, Romero-Severson J, Bernardo R. 2002. Chromosomal regions associated with segregation distortion in maize. Theoretical and Applied Genetics, 105, 622–628.
Mansur L M, Lark K G, Kross H, Oliveira A. 1993. Interval mapping of quantitative trait loci for reproductive, morphological, and seed traits of soybean [Glycine max (L.) Merr.]. Theoretical and Applied Genetics, 86, 907–913.
Mansur L M, Orf J H, Chase K, Jarvik T, Cregan P B, Lark K G. 1996. Genetic mapping of agronomic traits using recombinant inbred lines of soybean. Crop Science, 36, 1327–1336.
McGinnis K M, Thomas S G, Soule J D, Strader L C, Zale J M, Sun T P, Steber C M. 2003. The Arabidopsis SLEEPY1 gene encodes a putative F-box subunit of an SCF E3 ubiquitin ligase. The Plant Cell, 15, 1120–1130.
Mckenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M. 2010. The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research, 20, 1297–1303.
Miranda C, Scaboo A, Cober E, Denwar N, Bilyeu K. 2020. The effects and interaction of soybean maturity gene alleles controlling flowering time, maturity, and adaptation in tropical environments. BMC Plant Biology, 20, 65.
Oki N, Sayama T, Ishimoto M, Yokota I, Kaga A, Takahashi M, Takahashi M. 2018. Quantitative trait loci associated with short inter-node length in soybean. Breeding Science, 68, 554–560.
Panthee D R, Pantalone V R, Saxton A M, West D R, Sams C E. 2007. Quantitative trait loci for agronomic traits in soybean. Plant Breeding, 126, 51–57.
Shen Y T, Liu J, Geng H Y, Zhang J X, Liu Y C, Zhang H K, Xing S L, Du J C, Ma S S, Tian Z X. 2018. De novo assembly of a Chinese soybean genome. Science China (Life Sciences), 61, 871–884.
Slattery R A, Pritzl S, Reinwand K, Trautschold B, Sandhu D. 2011. Mapping eight male-sterile, female-sterile soybean mutants. Crop Science, 51, 231–236.
Song Q J, Hyten D L, Jia G F, Quigley C V, Fickus E W, Nelson R L, Cregan P B. 2013. Development and evaluation of SoySNP50K, a high-density genotyping array for soybean. PLoS ONE, 8, e54985.
Song Q J, Jenkins J, Jia G F, Hyten D L, Pantalone V, Jackson S A, Schmutz J, Cregan P B. 2016. Construction of high resolution genetic linkage maps to improve the soybean genome sequence assembly Glyma1.01. BMC Genomics, 17, 33.
Spartz A K, Lee S H, Wenger J P, Gonzalez N, Itoh H, Inzé D, Peer W A, Murphy A S, Overvoorde P J, Gray W M. 2012. The SAUR19 subfamily of small auxin up RNA genes promote cell expansion. The Plant Journal, 70, 978–990.
Specht J E, Chase K, Macrander M, Graef G L, Chung J, Markwell J P, Germann M, Orf J H, Lark K G. 2001. Soybean response to water: A QTL analysis of drought tolerance. Crop Science, 41, 493–509.
Speth B, Rogers J P, Boonyoo N, VanMeter A J, Baumbach J, Ott A, Moore J, Cina T, Palmer R, Sandhu D. 2015. Molecular mapping of five soybean genes involved in male-sterility, female-sterility. Genome, 58, 143–149.
Stoelting K N, Nipper R, Lindtke D, Caseys C, Waeber S, Castiglione S, Lexer C. 2013. Genomic scan for single nucleotide polymorphisms reveals patterns of divergence and gene flow between ecologically divergent species. Molecular Ecology, 22, 842–855.
Sun D S, Li W B, Zhang Z C, Chen Q S, Ning H L, Qiu L J, Sun G L. 2006. Quantitative trait loci analysis for the developmental behavior of soybean (Glycine max L. Merr.). Theoretical and Applied Genetics, 112, 665–673.
Tian Z X, Wang X B, Lee R, Li Y H, Specht J E, Nelson R L, McClean P E, Qiu L J, Ma J X. 2010. Artificial selection for determinate growth habit in soybean. Proceedings of the National Academy of Sciences of the United States of America, 107, 8563–8568.
Wang B B, Zhu Y B, Zhu J J, Liu Z P, Liu H, Dong X M, Guo J J, Li W, Chen J, Gao C, Zheng X M, E L Z, Lai J S, Zhao H M, Song W B. 2018. Identification and fine-mapping of a major maize leaf width QTL in a re-sequenced large recombinant inbred lines population. Frontiers in Plant Science, 9, 101.
Wang D, Graef G L, Procopiuk A M, Diers B W. 2004. Identification of putative QTL that underlie yield in interspecific soybean backcross populations. Theoretical and Applied Genetics, 108, 458–467.
Wang W B, Liu M F, Wang Y F, Li X L, Cheng S X, Shu L P, Yu Z P, Kong J J, Zhao T J, Gai J Y. 2016. Characterizing two inter-specific Bin maps for the exploration of the QTLs/genes that confer three soybean evolutionary traits. Frontiers in Plant Science, 7, 1248.
Xie W B, Feng Q, Yu H H, Huang X H, Zhao Q A, Xing Y Z, Yu S B, Han B, Zhang Q F. 2010. Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing. Proceedings of the National Academy of Sciences of the United States of America, 107, 10578–10583.
Xu X Y, Zeng L, Tao Y, Tri V, Wan J R, Boerma R, Noe J, Li Z L, Finnerty S, Pathan S M, Shannon J G, Nguyen H T. 2013. Pinpointing genes underlying the quantitative trait loci for root-knot nematode resistance in palaeopolyploid soybean by whole genome resequencing. Proceedings of the National Academy of Sciences of the United States of America, 110, 13469–13474.
Yang Z J, Chen Z Y, Peng Z S, Yu Y, Liao M L, Wei S H. 2017. Development of a high-density linkage map and mapping of the three-pistil gene (Pis1) in wheat using GBS markers. BMC Genomics 18, 567.
Yu H H, Xie W B, Wang J, Zhong X Y, Xu C G, Li X H, Xiao J H, Zhang Q F. 2011. Gains in QTL detection using an ultra-high density SNP map based on population sequencing relative to traditional RFLP/SSR markers. PLoS ONE, 6, e17595.
Zhang C, Wang P, Tang D, Yang Z, Lu F, Qi J, Tawari N R, Shang Y, Li C, Huang S. 2019. The genetic basis of inbreeding depression in potato. Nature Genetics, 51, 374–378.
Zhang W K, Wang Y J, Luo G Z, Zhang J S, He C Y, Wu X L, Gai J Y, Chen S Y. 2004. QTL mapping of ten agronomic traits on the soybean (Glycine max L. Merr.) genetic map and their association with EST markers. Theoretical and Applied Genetics, 108, 1131–1139.
Zhang X L, Wang W B, Guo N, Zhang Y Y, Bu Y P, Zhao J M, Xing H. 2018. Combining QTL-seq and linkage mapping to fine map a wild soybean allele characteristic of greater plant height. BMC Genomics, 19, 226.
Zhou Z K, Jiang Y, Wang Z, Gou Z, Lyu J, Li W Y, Yu Y J, Shu L P, Zhao Y J, Ma Y M, Fang C, Shen Y T, Liu T F, Li C C, Li Q, Wu M, Wang M, Wu Y S, Dong Y, Wan W T, et al. 2015. Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean. Nature Biotechnology, 33, 408–414.
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