QTL mapping and epistatic effect analysis of seedling height based on single segment substitution lines in rice
-
摘要:目的
挖掘控制水稻苗高的稳定QTL,并分析其上位性效应,为水稻苗高的分子育种提供QTL和理论参考。
方法以IR65598-112-2为供体、优良品种‘华粳籼74’为受体的单片段代换系(Single segment substitution line,SSSL)为材料,通过测定SSSL与‘华粳籼74’的苗高差异,对苗高QTL进行定位;通过代换作图缩小QTL的区间,并分析2个苗高QTL的上位性效应。
结果在第3号染色体长臂端定位到2个相邻的苗高QTLs (qSH3-1和qSH3-2),分别位于第3号染色体的32.59—33.08 Mb和33.16—34.81 Mb区间,长度分别为0.49和1.65 Mb;加性效应分别为−0.86和−1.09 cm;加性效应表型贡献值分别为−4.14%和−5.15%;包含这2个QTL的SSSL的苗高与‘华粳籼74’无显著差异。
结论本研究定位到2个苗高QTL,这2个QTL之间可能存在显著的上位性。
Abstract:ObjectiveTo find out the stable QTLs controlling rice seedling height, analyze their epistatic effects, and provide QTL and theoretical references for molecular breeding of rice seedling height.
MethodThe single segment substitution lines (SSSLs) with IR65598-112-2 as donor and ‘Huajingxian 74’ as receptor were used as materials. The difference of seedling height between SSSL and ‘Huajingxian 74’ was measured, and the QTLs of seedling height were mapped. The QTL interval was narrowed by substitution mapping, and the epistatic effects of two seedling height QTLs were also analyzed.
ResultTwo adjacent QTLs (qSH3-1 and qSH3-2) for seedling height were mapped on the long arm of chromosome 3, which were located in the intervals of 32.59−33.08 and 33.16−34.81 Mb, with the lengths of 0.49 and 1.65 Mb, respectively. The additive effects were −0.86 and −1.09 cm, respectively. The phenotypic contribution rate of additive effects were −4.14% and −5.15%, respectively. However, there was no significant difference of seedling height between SSSL harboring these two QTLs and ‘Huajingxian 74’.
ConclusionTwo QTLs for seedling height were identified, and there may be significant epistasis effects between the two QTLs.
-
-
表 1 试验SSSLs的信息
Table 1 Information of testing SSSLs
SSSL 供体
Donor染色体
Chromosome代换片段
Substitution segment片段位置/Mb
Segment positionK1 IR65598-112-2 3 3C52-5—3C33.13 31.76—33.08 K6 IR65598-112-2 3 3C52-5—3C32.70 31.69—32.59 K11 IR65598-112-2 3 3C52-7—3C34.90 33.16—34.81 K13 IR65598-112-2 3 3C52-5—3C34.90 31.69—34.81 表 2 用于检测代换片段的分子标记
Table 2 Molecular markers for screening of substitution segments
引物
Primer染色体
Chromosome位置/Mb
Position正向序列(5′→3′)
Forward sequence反向序列(5′→3′)
Reverse sequence3C52-5 3 31.69 ATTCTATGCCGCCAACCAA GAATTGTCAACTTCAGCATCCC 3C31.83 3 31.83 GATGTCAGGGAAAGAAGAAAC GCATTCTGGGTCAACATACAC 3C31.93 3 31.93 AGAAGGCAAACGGCTGACAAAG CGTGCTGAACTGGAGATACAAA 3C32.10 3 32.10 CCTTTGAACCTCGTGGGC TGGTGCGGGAACCCTATC 3C52-3 3 32.24 TACAGCCTCCTAATAGCATTGACC TCGAAGCTGCCGGTGTTG 3C32.48 3 32.48 CGCAGGAACAAACAACGA GAGGGAGTAATGGATACGAAGA 3C32.70 3 32.70 CCATCTCATTTATCAAGTCAA AGCCGTCTCGGGAGTGTA 3C52-6 3 32.91 GAGCATAAAGGCATTGGTTG TACCGTTTGTTCGGATAGATG 3C33.03 3 33.03 GCACTCGCCATCCTGACA CATTAGCTCGCTTCGTTT 3C33.13 3 33.13 GGAAACTTTGGTTGTCCCTGC TTGGAGCGTCGTTTGTGC 3C52-7 3 33.19 AGAACACCCGCTCCATCG AGCAGCACGCAGCCGCCTT RM130 3 33.39 TGTTGCTTGCCCTCACGAAG GGTCGCGTGCTTGGTTTTGGTTC 3C34.25 3 34.25 GAACTGATACGGTAGGATG GATGGACACGGACTCTTT 3C52-8 3 34.61 GACGAGGAGGAGGAAGAGGA AGCAATCGGAGCAGCAAGAG 3C34.72 3 34.72 TGGAGGAATCAAGGAGAC ATTGAGAAAGAGGCGTAA 3C34.90 3 34.90 TCAGCAAACAATCTACTACCGC ACAGGACGCACTCAACAT 3C35.15 3 35.15 TTGCTGCGGTGGACCTCTTT CGGCACCAGTGGGGACAT 3C35.39 3 35.39 TGCTCGGGAACCAGACGT TGAATCCTGCTGCTTTGA 3C52-4 3 35.74 TGAACCAATGGAAACCTTGA GTCCCTGTATGCGGATGAT 表 3 苗高QTL的加性效应与加性效应表型贡献率1)
Table 3 Additive effect and additive effect phenotypic contribution rate of QTL in seedling height
SSSL QTL 染色体
Chromosome位置/Mb
Position3次试验的加性效应/cm
Additive effects of three tests整体加性效应/cm
Average additive
effect表型贡献率/%
Phenotypic
contribution rate1 2 3 K1 qSH3-1 3 31.76—33.08 −1.57 - −0.27 −0.86** −4.14 K11 qSH3-2 3 33.16—34.81 −0.75 −0.62 −1.33 −1.09** −5.15 1) “**”表示K1、K11与‘华粳籼74’的苗高在P < 0.01水平差异极显著(t检验);“—”表示未检测到QTL;负效应“−”表示受体表型值减小
1) “**” indicates that the seedling heights of K1 and K11 are highly significantly different from that of ‘Huajingxian 74’ at P < 0.01 (t test); “—” indicates that no QTL is detected; Negative effect “−” indicates a decrease in receptor phenotype value表 4 qSH3-1和qSH3-2区间内CDS和启动子区域都发生变异的基因
Table 4 Variation genes in both CDS and promoter regions in qSH3-1 and qSH3-2 intervals
QTL 变异类型
Variation type基因名称
Gene nameqSH3-1 密码子改变和删除
Codon change and deletionOs03g0793300、Os03g0786600 密码子删除 Codon deletion Os03g0785200 密码子插入 Codon insertion Os03g0785800、Os03g0787000、Os03g0791432、Os03g0792300 移码 Frame shift Os03g0788000、Os03g0790000、Os03g0793100、Os03g0793700 qSH3-2 密码子改变和删除
Codon change and deletionOs03g0800200、Os03g0800500、Os03g0809400、Os03g0812800、Os03g0816000、Os03g0820700 密码子删除 Codon deletion Os03g0796900、Os03g0797500、Os03g0798400、Os03g0802900、Os03g0810800、Os03g0811400、Os03g0812400、Os03g0816500、Os03g0816700、Os03g0821200、Os03g0825900 密码子插入 Codon insertion Os03g0800900、Os03g0801800、Os03g0802700、Os03g0817200、Os03g0823400、Os03g0824650、Os03g0828300 密码子插入/剪接位点区域
Codon insertion/splice site regionOs03g0828500 移码 Frame shift Os03g0814500、Os03g0824300、 Os03g0824400、Os03g0826600 起始密码子缺失 Start codon lost Os03g0815100 终止密码子缺失 Stop codon lost Os03g0821250 -
[1] 胡卫安. 水稻直播栽培技术推广意义及措施[J]. 世界热带农业信息, 2020(12): 10-11. doi: 10.3969/j.issn.1009-1726.2020.12.006 [2] 刘朝志. 水稻直播栽培存在问题及对策[J]. 现代农村科技, 2019(5): 23. doi: 10.3969/j.issn.1674-5329.2019.05.019 [3] DIMAANO N G B, ALI J, MAHENDER A, et al. Identification of quantitative trait loci governing early germination and seedling vigor traits related to weed competitive ability in rice[J]. Euphytica, 2020, 216(10): 159. doi: 10.1007/s10681-020-02694-8.
[4] ZHANG Z, YU S, YU T, et al. Mapping quantitative trait loci (QTLs) for seedling-vigor using recom binant inbred lines of rice (Oryza sativa L. )[J]. Field Crops Research, 2005, 91(2): 161-170.
[5] DIWAN J R, CHANNBYREGOWDA M, SHENOY V, et al. Molecular mapping of early vigour related QTLs in rice[J]. Research & Reviews: Journal of Biology, 2013, 1: 24-30.
[6] SINGH U M, YADAV S, DIXIT S, et al. QTL hotspots for early vigor and related traits under dry direct-seeded system in rice (Oryza sativa L. )[J]. Frontiers in Plant Science, 2017, 8: 286. doi: 10.3389/fpls.2017.00286.
[7] RAO A N, JOHNSON D E, SIVAPRASAD B, et al. Weed management in direct-seeded rice[M]. Advances in Agronomy, 2007, 93: 153-255.
[8] 闫晓霞, 王丰, 柳武革, 等. 水稻直播适应性的遗传基础与育种策略[J]. 广东农业科学, 2022, 49(1): 1-13. doi: 10.16768/j.issn.1004-874X.2022.01.001 [9] 马雅美, 张少红, 赵均良. 水稻直播相关性状遗传分析及分子机制研究进展[J]. 广东农业科学, 2021, 48(10): 13-22. doi: 10.16768/j.issn.1004-874X.2021.10.002 [10] REDOÑA E D, MACKILL D J. Mapping quantitative trait loci for seedling vigor in rice using RFLPs[J]. Theoretical and Applied Genetics, 1996, 92(3/4): 395-402.
[11] EIZENGA G C, NEVES P C F, BRYANT R J, et al. Evaluation of a M-202 × Oryza nivara advanced backcross mapping population for seedling vigor, yield components and quality[J]. Euphytica, 2016, 208(1): 157-171. doi: 10.1007/s10681-015-1613-y
[12] ZHANG A P, LIU C L, CHEN G, et al. Genetic analysis for rice seedling vigor and fine mapping of a major QTL qSSL1b for seedling shoot length[J]. Breeding Science, 2017, 67(3): 307-315. doi: 10.1270/jsbbs.16195
[13] LU X, NIU A, CAI H, et al. Genetic dissection of seedling and early vigor in a recombinant inbred line population of rice[J]. Plant Science, 2007, 172(2): 212-220. doi: 10.1016/j.plantsci.2006.08.012
[14] KARLA I C L, HYUNJUNG K, THOMAS H T. Identification of seedling vigor-associated quantitative trait loci in temperate japonica rice[J]. Plant Breeding and Biotechnology, 2016, 4(4): 426-440. doi: 10.9787/PBB.2016.4.4.426
[15] CAIRNS J E, NAMUCO O S, TORRES R, et al. Investigating early vigour in upland rice ( Oryza sativa L. ): Part II: Identification of QTLs controlling early vigour under greenhouse and field conditions[J]. Field Crops Research, 2009, 113(3): 207-217. doi: 10.1016/j.fcr.2009.05.007
[16] MANANGKIL O E, VU H T T, MORI N, et al. Mapping of quantitative trait loci controlling seedling vigor in rice (Oryza sativa L. ) under submergence[J]. Euphytica, 2013, 192(1): 63-75. doi: 10.1007/s10681-012-0857-z
[17] ABE A, TAKAGI H, FUJIBE T, et al. OsGA20ox1, a candidate gene for a major QTL controlling seedling vigor in rice[J]. Theoretical and Applied Genetics, 2012, 125(4): 647-657. doi: 10.1007/s00122-012-1857-z
[18] ZHOU L, WANG J, YI Q, et al. Quantitative trait loci for seedling vigor in rice under field conditions[J]. Field Crops Research, 2007, 100(2/3): 294-301.
[19] WU B, MAO D, LIU T, et al. Two quantitative trait loci for grain yield and plant height on chromosome 3 are tightly linked in coupling phase in rice[J]. Molecular Breeding, 2015, 35(8): 156. doi: 10.1007/s11032-015-0345-y.
[20] 包劲松, 何平, 夏英武, 等. 不同发育阶段水稻苗高的QTL分析[J]. 遗传, 1999(5): 38-40. doi: 10.3321/j.issn:0253-9772.1999.05.012 [21] 杨习武, 高云, 顾后文, 等. 基于染色体单片段代换系的水稻苗期氮利用相关QTL鉴定[J]. 扬州大学学报(农业与生命科学版), 2020, 41(5): 1-8. doi: 10.16872/j.cnki.1671-4652.2020.05.001 [22] 孔迎春, 张燎. 两种肥力水平下水稻苗高QTL的比较分析[J]. 武汉植物学研究, 2005(2): 121-124. [23] ZHAO Y, JIANG C H, REHMAN R M A, et al. Genetic analysis of roots and shoots in rice seedling by association mapping[J]. Genes & Genomics, 2019, 41(1): 95-105.
[24] CHEN K, ZHANG Q, WANG C C, et al. Genetic dissection of seedling vigour in a diverse panel from the 3, 000 Rice (Oryza sativa L. ) Genome Project[J]. Scientific Reports, 2019, 9: 4804. doi: 10.1038/s41598-019-41217-x.
[25] DANG X, THI T G T, DONG G, et al. Genetic diversity and association mapping of seed vigor in rice (Oryza sativa L. )[J]. Planta, 2014, 239(6): 1309-1319. doi: 10.1007/s00425-014-2060-z
[26] LU Q, ZHANG M, NIU X, et al. Uncovering novel loci for mesocotyl elongation and shoot length in indica rice through genome-wide association mapping[J]. Planta, 2016, 243(3): 645-657. doi: 10.1007/s00425-015-2434-x
[27] YANG J, GUO Z, LUO L, et al. Identification of QTL and candidate genes involved in early seedling growth in rice via high-density genetic mapping and RNA-seq[J]. The Crop Journal, 2021, 9(2): 360-371. doi: 10.1016/j.cj.2020.08.010
[28] ZENG M S, YANG J, WU K J, et al. Genome-wide association study reveals early seedling vigour-associated quantitative trait loci in indica rice[J]. Euphytica, 2021, 217(7): 141. doi: 10.1007/s10681-021-02868-y.
[29] 杨梯丰, 张子怡, 董景芳, 等. 水稻低温发芽力QTL qLTG3-1基因内分子标记的开发及其在华南籼稻中的应用评价[J]. 广东农业科学, 2021, 48(10): 32-41. [30] WISSUWA M, WEGNER J, AE N, et al. Substitution mapping of Pup1: A major QTL increasing phosphorus uptake of rice from a phosphorus-deficient soil[J]. Theoretical and Applied Genetics, 2002, 105(6/7): 890-897.
[31] ESHED Y, ZAMIR D. An introgression line population of Lycopersicon pennellii in the cultivated tomato enables the identification and fine mapping of yield-associated QTL[J]. Genetics, 1995, 141(3): 1147-1162. doi: 10.1093/genetics/141.3.1147
[32] 赵芳明, 张桂权, 曾瑞珍, 等. 利用单片段代换系研究水稻产量相关性状QTL加性及上位性效应[J]. 作物学报, 2012, 38(11): 2007-2014. [33] YANO K, TAKASHI T, NAGAMATSU S, et al. Efficacy of microarray profiling data combined with QTL mapping for the identification of a QTL gene controlling the initial growth rate in rice[J]. Plant & Cell Physiology, 2012, 53(4): 729-739.
[34] TANKSLEY S D. Mapping polygenes[J]. Annual Review of Genetics, 1993, 27: 205-233. doi: 10.1146/annurev.ge.27.120193.001225