QTL-Seq Identified a Major QTL for Grain Length and Weight in Rice Using Near Isogenic F2 Population
Received date: 2018-01-15
Accepted date: 2018-03-13
Online published: 2018-03-07
Mapping and isolation of quantitative trait loci (QTLs) or genes controlling grain size or weight is very important to uncover the molecular mechanisms of seed development and crop breeding. To identify the QTLs controlling grain size and weight, we developed a near isogenic line F2 (NIL-F2) population, which was derived from a residual heterozygous plant in an F7 generation of recombinant inbred line (RIL). With the completion of more than 30× whole genome re-sequencing of the parents, two DNA bulks for large and small grains, a total of 58.94 Gb clean nucleotide data were generated. A total of 455 262 single nucleotide polymorphisms (SNPs) between the parents were identified to perform bulked QTL-seq. A candidate genomic region containing SNPs strongly associated with grain length and weight was identified from 15 to 20 Mb on chromosome 5. We designated the major QTL in the candidate region as qTGW5.3. Then, qTGW5.3 was further validated with PCR-based conventional QTL mapping method through developing simple sequence repeat and Insertion/Deletion markers in the F2 population. Furthermore, recombinants and the progeny tests delimited the candidate region of qTGW5.3 to 1.13 Mb, flanked by HX5009 (15.15 Mb) and HX5003 (16.28 Mb). A set of NILs, selected from the F2 population, was developed to evaluate the genetic effect of qTGW5.3. Significant QTL effects were detected on grain length, grain width and 1000-grain weight of H12-29 allele with 1.14 mm, -0.11 mm and 3.11 g, which explained 99.64%, 95.51% and 97.32% of the phenotypic variations, respectively.
Yaobin Qin, Peng Cheng, Yichen Cheng, Yue Feng, Derun Huang, Tingxu Huang, Xianjun Song, Jiezheng Ying . QTL-Seq Identified a Major QTL for Grain Length and Weight in Rice Using Near Isogenic F2 Population[J]. Rice Science, 2018 , 25(3) : 121 -131 . DOI: 10.1016/j.rsci.2018.04.001
| [1] | Abe A, Kosugi S, Yoshida K, Natsume S, Takagi H, Kanzaki H, Matsumura H, Yoshida K, Mitsuoka C, Tamiru M, Innan H, Cano L, Kamoun S, Terauchi R.2012. Genome sequencing reveals agronomically important loci in rice using MutMap.Nat Biotechnol, 30: 174-178. |
| [2] | Austin R S, Vidaurre D, Stamatiou G, Breit R, Provart N J, Bonetta D, Zhang J, Fung P, Gong Y, Wang P W, McCourt P, Guttman D S.2011. Next-generation mapping ofArabidopsis genes. Plant J, 67(4): 715-725. |
| [3] | Bai X F, Wu B, Xing Y Z.2012. Yield-related QTLs and their applications in rice genetic improvement.J Integr Plant Biol, 54(5): 300-311. |
| [4] | Bhatia D, Wing R A, Yu Y, Chougule K, Kudrna D, Lee S, Rang A, Singh K.2018. Genotyping by sequencing of rice interspecific backcross inbred lines identifies QTLs for grain weight and grain length.Euphytica, 214: 41. |
| [5] | Chen X, Temnykh S, Xu Y, Cho Y G, McCouch S R.1997. Development of a microsatellite framework map providing genome-wide coverage in rice (Oryza sativa L.). Theor Appl Genet, 95(4): 553-567. |
| [6] | Cheng S H, Zhuang J Y, Fan Y Y, Du J H, Cao L Y.2007. Progress in research and development on hybrid rice: A super-domesticate in China.Ann Bot, 100(5): 959-966. |
| [7] | Daware A, Das S, Srivastava R, Badoni S, Singh A K, Agarwal P, Parida S K, Tyagi A K.2016. An efficient strategy combining SSR markers- and advanced QTL-seq-driven QTL mapping unravels candidate genes regulating grain weight in rice.Front Plant Sci, 7: 1535. |
| [8] | Duan P G, Xu J S, Zeng D L, Zhang B L, Geng M F, Zhang G Z, Huang K, Huang L J, Xu R, Ge S, Qian Q, Li Y H.2017. Natural variation in the promoter ofGSE5 contributes to grain size diversity in rice. Mol Plant, 10(5): 685-694. |
| [9] | Ehrenreich I M, Torabi N, Jia Y, Kent J, Martis S, Shapiro J A, Gresham D, Caudy A A, Kruglyak L.2010. Dissection of genetically complex traits with extremely large pools of yeast segregants.Nature, 464: 1039-1042. |
| [10] | Fang Y X, Wu W M, Zhang X Q, Jiang H, Lu W Y, Pan J J, Hu J, Guo L B, Zeng D L, Xue D W.2015. Identification of quantitative trait loci associated with tolerance to low potassium and related ions concentrations at seedling stage in rice (Oryza sativa L.). Plant Growth Regul, 77(2): 157-166. |
| [11] | Giovannoni J J, Wing R A, Ganal M W, Tanksley S D.1991. Isolation of molecular markers from specific chromosomal intervals using DNA pools from existing mapping populations.Nucl Acids Res, 19: 6553-6558. |
| [12] | Huang H X, Qian Q.2017. Progress in genetic research of rice grain shape and breeding achievements of long-grain shape and good qualityjaponica rice. Chin J Rice Sci, 31(6): 665-672. (in Chinese with English abstract) |
| [13] | Huang K, Wang D K, Duan P G, Zhang B L, Xu R, Li N, Li Y H.2017. WIDE AND THICK GRAIN 1, which encodes an otubain- like protease with deubiquitination activity, influences grain size and shape in rice.Plant J, 91(5): 849-860. |
| [14] | Illa-Berenguer E, van Houten J, Huang Z, van der Knaap E.2015. Rapid and reliable identification of tomato fruit weight and locule number loci by QTL-seq.Theor Appl Genet, 128(7): 1329-1342. |
| [15] | Li D Y, Huang Z Y, Song S H, Xin Y Y, Mao D H, Lv Q M, Zhou M, Tian D M, Tang M F, Wu Q, Liu X, Chen T T, Song X W, Fu X Q, Zhao B R, Liang C Z, Li A H, Liu G Z, Li S G, Hu S N, Cao X F, Yu J, Yuan L P, Chen C Y, Zhu L H.2016. Integrated analysis of phenome, genome, and transcriptome of hybrid rice uncovered multiple heterosis-related loci for yield increase.Proc Natl Acad Sci USA, 113: 6026-6035. |
| [16] | Li H, Durbin R.2009. Fast and accurate short read alignment with Burrows-Wheeler transform.Bioinformatics, 25: 1754-1760. |
| [17] | Li N, Li Y H.2016. Signaling pathways of seed size control in plants.Curr Opin Plant Biol, 33: 23-32. |
| [18] | Lu H F, Lin T, Klein J, Wang S H, Qi J J, Zhou Q, Sun J J, Zhang Z H, Weng Y Q, Huang S W.2014. QTL-seq identifies an early flowering QTL located near flowering locusT in cucumber. Theor Appl Genet, 127(7): 1491-1499. |
| [19] | Lu X, Xiong Q, Cheng T, Li Q T, Liu X L, Bi Y D, Li W, Zhang W K, Ma B, Lai Y C, Du W G, Man W Q, Chen S Y, Zhang J S.2017. APP2C-1 allele underlying a quantitative trait locus enhances soybean 100-seed weight. Mol Plant, 10(5): 670-684. |
| [20] | Michelmore R W, Paran I, Kesseli R V.1991. Identification of markers linked to disease-resistance genes by bulked segregant analysis: A rapid method to detect markers in specific genomic regions by using segregating populations.Proc Natl Acad Sci USA, 88: 9828-9832. |
| [21] | Murray M G, Thompson W F.1980. Rapid isolation of high molecular weight plant DNA.Nucl Acids Res, 8: 4321-4325. |
| [22] | Ogiso-Tanaka E, Tanaka T, Tanaka K, Nonoue Y, Sasaki T, Fushimi E, Koide Y, Okumoto Y, Yano M, Saito H.2017. Detection of novel QTLs qDTH4.5 and qDTH6.3, which confer late heading under short-day conditions, by SSR marker-based and QTL-seq analysis. Breeding Sci, 67: 101-109. |
| [23] | Schneeberger K, Ossowski S, Lanz C, Juul T, Petersen A H, Nielsen K L, Jorgensen J E, Weigel D, Andersen S U.2009. SHOREmap: Simultaneous mapping and mutation identification by deep sequencing.Nat Methods, 6(8): 550-551. |
| [24] | Schneeberger K, Weigel D.2011. Fast-forward genetics enabled by new sequencing technologies.Trends Plant Sci, 16(5): 282-288. |
| [25] | Shao G N, Tang S Q, Luo J, Jiao G A, Wei X J, Tang A, Wu J L, Zhuang J Y, Hu P S.2010. Mapping ofqGL7-2, a grain length QTL on chromosome 7 of rice. J Genet Genom, 37(8): 523-531. |
| [26] | Song X J, Kuroha T, Ayano M, Furuta T, Nagai K, Komeda N, Segami S, Miura K, Ogawa D, Kamura T, Suzuki T, Higashiyama T, Yamasaki M, Mori H, Inukai Y, Wu J, Kitano H, Sakakibara H, Jacobsen S E, Ashikari M.2015. Rare allele of a previously unidentified histone H4 acetyltransferase enhances grain weight, yield, and plant biomass in rice.Proc Natl Acad Sci USA, 112(1): 76-81. |
| [27] | 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.2013. SLAF-seq: An efficient method of large-scale de novo SNP discovery and genotyping using high-throughput sequencing. PLoS One, 8: e58700. |
| [28] | Takagi H, Abe A, Yoshida K, Kosugi S, Natsume S, Mitsuoka C, Uemura A, Utsushi H, Tamiru M, Takuno S, Innan H, Cano L M, Kamoun S, Terauchi R.2013. QTL-seq: Rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations.Plant J, 74(1): 174-183. |
| [29] | Wang S S, Wu K, Qian Q, Liu Q, Li Q, Pan Y J, Ye Y F, Liu X Y, Wang J, Zhang J Q, Li S, Wu Y J, Fu X D.2017. Non-canonical regulation of SPL transcription factors by a human OTUB1-like deubiquitinase defines a new plant type rice associated with higher grain yield. Cell Res, 27: 1142-1156. |
| [30] | Wang Y X, Xiong G S, Hu J, Jiang L, Yu H, Xu J, Fang Y X, Zeng L J, Xu E, Xu J, Ye W J, Meng X B, Liu R F, Chen H Q, Jing Y H, Wang Y H, Zhu X D, Li J Y, Qian Q.2015. Copy number variation at the GL7 locus contributes to grain size diversity in rice. Nat Genet, 47: 944-948. |
| [31] | Yamanaka N, Watanabe S, Toda K, Hayashi M, Fuchigami H, Takahashi R, Harada K.2005. Fine mapping of the FT1 locus for soybean flowering time using a residual heterozygous line derived from a recombinant inbred line. Theor Appl Genet, 110(4): 634-639. |
| [32] | Yan W H, Wang P, Chen H X, Zhou H J, Li Q P, Wang C R, Ding Z H, Zhang Y S, Yu S B, Xing Y Z, Zhang Q F.2011. A major QTL,Ghd8, plays pleiotropic roles in regulating grain productivity, plant height, and heading date in rice. Mol Plant, 4: 319-330. |
| [33] | Yi C D, Wang D R, Jiang W, Li W, Cheng X J, Wang Y, Zhou Y, Liang G H, Gu M H.2016. Development of functional markers and identification of haplotypes for rice grain width gene GS5. Chin J Rice Sci, 30(5): 487-492. (in Chinese with English abstract) |
| [34] | Ying J Z, Shan J X, Gao J P, Zhu M Z, Shi M, Lin H X.2012. Identification of quantitative trait loci for lipid metabolism in rice seeds.Mol Plant, 5(4): 865-875. |
| [35] | Yoon D B, Kang K H, Kim H J, Ju H G, Kwon S J, Suh J P, Jeong O Y, Ahn S N.2006. Mapping quantitative trait loci for yield components and morphological traits in an advanced backcross population between Oryza grandiglumis and the O. sativa japonica cultivar Hwaseongbyeo. Theor Appl Genet, 112: 1052-1062. |
| [36] | Yu J P, Xiong H Y, Zhu X Y, Zhang H L, Li H H, Miao J L, Wang W S, Tang Z S, Zhang Z Y, Yao G X, Zhang Q, Pan Y H, Wang X, Rashid M A R, Li J J, Gao Y M, Li Z K, Yang W C, Fu X D, Li Z C.2017. OsLG3 contributing to rice grain length and yield was mined by Ho-LAMap.BMC Biol, 15: 28. |
| [37] | Zhang Y, Luo L J, Xu C, Zhang Q F, Xing Y Z.2006. Quantitative trait loci for panicle size, heading date and plant height co- segregating in trait-performance derived near-isogenic lines of rice (Oryza sativa). Theor Appl Genet, 113(2): 361-368. |
| [38] | Zuo J R, Li J Y.2014. Molecular genetic dissection of quantitative trait loci regulating rice grain size.Annu Rev Genet, 48: 99-118. |
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