Detection and analysis of QTL for panicle length in rice using a high-density genetic map

WEI Minyi; ZHANG Yuexiong; MA Zengfeng; HUANG Dahui; LIU Chi; QIN Yuanyuan; LU Yingping; YAN Liuhui; WU Zishuai; ZHOU Xiaolong; WU Xuxiang; QIN Gang

doi:10.7671/j.issn.1001-411X.202306061

Journal of South China Agricultural University > 2023 > 44(6): 889-895. > DOI: 10.7671/j.issn.1001-411X.202306061

WEI Minyi, ZHANG Yuexiong, MA Zengfeng, et al. Detection and analysis of QTL for panicle length in rice using a high-density genetic map[J]. Journal of South China Agricultural University, 2023, 44(6): 889-895. DOI: 10.7671/j.issn.1001-411X.202306061

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Detection and analysis of QTL for panicle length in rice using a high-density genetic map

1.
Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning 530007, China
2.
Agricultural Science and Technology Information Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
3.
Liuzhou Branch, Guangxi Academy of Agricultural Sciences/Liuzhou Research Center of Agricultural Sciences, Liuzhou 545000, China
4.
Guangdong Maoming Agriculture & Forestry Technical College, Maoming 525000, China

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Received Date: July 09, 2023
Available Online: November 12, 2023
Published Date: September 19, 2023

Graphical Abstract

Abstract

Abstract

Objective
To deeply explore new genes related to panicle length and provide a basis for the study of genetic mechanism of panicle length regulation and molecular breeding in rice.
Method
Two superior parents, ‘ZP37’ and ‘R8605’, as well as 208 recombinant inbred lines (RILs) derived from the cross of ZP37/R8605 were used as a mapping population to locate quantitative trait loci (QTLs) for panicle length in three different environments through the high-density linkage map of whole genome resequencing, and to analyze their pyramiding effects.
Result
A total of 11 QTLs for panicle length were detected on chromosomes 3, 4, 7, 8, 9 and 12, with the logs of odds (LODs) ranging from 3.07 to 12.87 and contribution rates ranging from 2.17% to 10.94%, seven of the QTLs were new loci, and the remaining four QTLs overlapped or were close to the reported panicle length genes and QTLs. Among them, four stable QTLs were detected repeatedly in two different environments, and by analyzing the lines that pyramiding different numbers of panicle length QTLs, the results showed that the panicle length QTLs showed an additive effect, and the increase in the number of QTLs significantly increased the panicle length of rice.
Conclusion
The results of this study provide a solid foundation for cloning and functional analysis of rice panicle length QTLs, as well as a theoretical basis and genetic resources for high-yield rice breeding.
- Oryza sativa L.,
- Spike length,
- QTL mapping,
- High-density genetic map

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References (41)

References

[1]	XING Y, ZHANG Q. Genetic and molecular bases of rice yield[J]. Annual Review of Plant Biology, 2010, 61: 421-442. doi: 10.1146/annurev-arplant-042809-112209
[2]	LI X, YAN W, AGRAMA H, et al. Mapping QTLs for improving grain yield using the USDA rice mini-core collection[J]. Planta, 2011, 234(2): 347-361. doi: 10.1007/s00425-011-1405-0
[3]	LIU T, LI L, ZHANG Y, et al. Comparison of quantitative trait loci for rice yield, panicle length and spikelet density across three connected populations[J]. Journal of Genetics, 2011, 90(2): 377-382. doi: 10.1007/s12041-011-0083-9
[4]	HUANG X, QIAN Q, LIU Z, et al. Natural variation at the DEP1 locus enhances grain yield in rice[J]. Nature Genetics, 2009, 41(4): 494-497. doi: 10.1038/ng.352
[5]	LI S, QIAN Q, FU Z, et al. Short panicle1 encodes a putative PTR family transporter and determines rice panicle size[J]. The Plant Journal, 2009, 58(4): 592-605. doi: 10.1111/j.1365-313X.2009.03799.x
[6]	LI F, LIU W, TANG J, et al. Rice DENSE AND ERECT PANICLE 2 is essential for determining panicle outgrowth and elongation[J]. Cell Research, 2010, 20(7): 838-849. doi: 10.1038/cr.2010.69
[7]	QIAO Y, PIAO R, SHI J, et al. Fine mapping and candidate gene analysis of dense and erect panicle 3, DEP3, which confers high grain yield in rice (Oryza sativa L.)[J]. Theoretical and Applied Genetics, 2011, 122(7): 1439-1449. doi: 10.1007/s00122-011-1543-6
[8]	LI M, TANG D, WANG K, et al. Mutations in the F-box gene LARGER PANICLE improve the panicle architecture and enhance the grain yield in rice[J]. Plant Biotechnology Journal, 2011, 9(9): 1002-1013. doi: 10.1111/j.1467-7652.2011.00610.x
[9]	LI X, QIAN Q, FU Z, et al. Control of tillering in rice[J]. Nature, 2003, 422(6932): 618-621. doi: 10.1038/nature01518
[10]	KOMATSU M, MAEKAWA M, SHIMAMOTO K, et al. The LAX1 and FRIZZY PANICLE 2 genes determine the inflorescence architecture of rice by controlling rachis-branch and spikelet development[J]. Developmental Biology, 2001, 231(2): 364-373. doi: 10.1006/dbio.2000.9988
[11]	LU Z, YU H, XIONG G, et al. Genome-wide binding analysis of the transcription activator IDEAL PLANT ARCHITECTURE 1 reveals a complex network regulating rice plant architecture[J]. The Plant Cell, 2013, 25(10): 3743-3759. doi: 10.1105/tpc.113.113639
[12]	YUAN H, QIN P, HU L, et al. OsSPL18 controls grain weight and grain number in rice[J]. Journal of Genetics and Genomics, 2019, 46(1): 41-51. doi: 10.1016/j.jgg.2019.01.003
[13]	CHO Y, KANG H, LEE J, et al. Identification of quantitative trait loci in rice for yield, yield components, and agronomic traits across years and locations[J]. Crop Science, 2007, 47(6): 2403-2417. doi: 10.2135/cropsci2006.08.0509
[14]	MARATHI B, GULERIA S, MOHAPATRA T, et al. QTL analysis of novel genomic regions associated with yield and yield related traits in new plant type based recombinant inbred lines of rice (Oryza sativa L.)[J]. BMC Plant Biology, 2012, 12(1): 137. doi: 10.1186/1471-2229-12-137
[15]	WEI M, LUO T, HUANG D, et al. Construction of high-density genetic map and QTL mapping for grain shape in the rice RIL population[J/OL]. Plants, 2023, 12(16): 2911. https://doi.org/10.3390/plants12162911.
[16]	MENG L, LI H, ZHANG L, et al. QTL IciMapping: Integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations[J]. The Crop Journal, 2015, 3: 269-283. doi: 10.1016/j.cj.2015.01.001
[17]	王建康. 数量性状基因的完备区间作图方法[J]. 作物学报, 2009, 35(2): 239-245.
[18]	MCCOUCH S, KOCHERT G, YU Z, et al. Molecular mapping of rice chromosomes[J]. Theoretical and Applied Genetics, 1988, 76(6): 815-829. doi: 10.1007/BF00273666
[19]	PAN Q, ALI F, YANG X, et al. Exploring the genetic characteristics of two recombinant inbred line populations via high-density SNP markers in maize[J]. PLoS One, 2012, 7(12): e52777. doi: 10.1371/journal.pone.0052777
[20]	CHEN Z, WANG B, DONG X, et al. An ultra-high density bin-map for rapid QTL mapping for tassel and ear architecture in a large F₂ maize population[J]. BMC Genomics, 2014, 15(1): 433. doi: 10.1186/1471-2164-15-433
[21]	GOLICZ A, BAYER P, EDWARDS D. Skim-based genotyping by sequencing[M]//Methods in Molecular Biology. New York: Springer New York, 2014: 257-270.
[22]	张亚东, 梁文化, 赫磊, 等. 水稻RIL群体高密度遗传图谱构建及粒型QTL定位[J]. 中国农业科学, 2021, 54(24): 5163-5176.
[23]	宋博文, 王朝欢, 赵哲, 等. 基于高密度遗传图谱对水稻粒形QTL定位及分析[J]. 作物学报, 2022, 48(11): 2813-2829.
[24]	闫晓霞, 朱满山, 王丰, 等. 利用高密度遗传图谱定位水稻耐低氧萌发QTL[J]. 广东农业科学, 2023, 50(4): 13-21.
[25]	潘俊峰, 崔克辉, 刘彦卓, 等. 利用高密度Bin图谱定位水稻叶绿素含量QTL[J]. 广东农业科学, 2022, 49(9): 132-140.
[26]	ZHANG M, ZHOU Z, CHEN Y, et al. Finding new addictive QTL for yield traits based on a high-density genetic map in hybrid rice[J]. Plant Growth Regultion, 2021, 93: 105-115. doi: 10.1007/s10725-020-00669-2
[27]	LI X, WU L, WANG J, et al. Genome sequencing of rice subspecies and genetic analysis of recombinant lines reveals regional yield- and quality-associated loci[J]. BMC Biology, 2018, 16: 102. doi: 10.1186/s12915-018-0572-x
[28]	XING Z, TAN F, HUA P, et al. Characterization of the main effects, epistatic effects and their environmental interactions of QTLs on the genetic basis of yield traits in rice[J]. Theoretical and Applied Genetics, 2002, 105(2/3): 248-257. doi: 10.1007/s00122-002-0952-y
[29]	贾佩陇, 李彪, 黎明辉, 等. 基于水稻染色体片段代换系的苗期耐低氮QTL分析[J]. 华南农业大学学报, 2019, 40(4): 16-24.
[30]	陈燕华, 黄大辉, 邱永福, 等. 水稻主要农艺性状的QTL分析[J]. 华南农业大学学报, 2014, 35(5): 42-51.
[31]	淳雁, 李学勇. 水稻穗型的遗传调控研究进展[J]. 植物学报, 2017, 52(1): 19-29.
[32]	LIU E B, LIU Y, WU G C, et al. Identification of a candidate gene for panicle length in rice (Oryza sativa L.) via association and linkage analysis[J]. Frontiers in Plant Science, 2016, 7: 596.
[33]	徐华山, 孙永建, 周红菊, 等. 构建水稻优良恢复系背景的重叠片段代换系及其效应分析[J]. 作物学报, 2007, 33(6): 979-986.
[34]	魏少博, PRIYA L, 王文生, 等. 两个水稻骨干恢复系重要农艺性状的遗传基础研究[J]. 植物遗传资源学报, 2017, 18(5): 801-809.
[35]	ZHANG L, WANG J, WANG J, et al. Quantitative trait locus analysis and fine mapping of the qPL6 locus for panicle length in rice[J]. Theoretical and Applied Genetics, 2015, 128(6): 1151-1161. doi: 10.1007/s00122-015-2496-y
[36]	FUJITA D, TRIJATMIKO K, TAGLE A, et al. NAL1 allele from a rice landrace greatly increases yield in modern indica cultivars[J]. Proceedings of the National Academy of Sciences of the United States of America, 2013, 110(51): 20431-20436.
[37]	ZHANG G, LI S, WANG L, et al. LSCHL4 from Japonica cultivar, which is allelic to NAL1, increases yield of Indica super rice 93-11[J]. Molecular Plant, 2014(8): 1350-1364.
[38]	KUMAR A, DIXIT S, RAM T, et al. Breeding high-yielding drought-tolerant rice: Genetic variations and conventional and molecular approaches[J]. Journal of Experimental Botany, 2014, 65(21): 6265-6278.
[39]	韦敏益, 黄大辉, 张月雄, 等. 分子标记辅助选育香型优质稻新品种‘桂野香占’[J/OL]. 分子植物育种, 2021: 1-18. (2021-09-28) [2023-07-01]. http://kns.cnki.net/kcms/detail/46.1068.S.20210928.0926.012.html.
[40]	ZONG G, WANG A, WANG L, et al. A pyramid breeding of eight grain-yield related quantitative trait loci based on marker-assistant and phenotype selection in rice (Oryza sativa L.)[J]. Journal of Genetics and Genomics, 2012, 39(7): 335-350. doi: 10.1016/j.jgg.2012.06.004
[41]	MALLIKARJUNA S, AHMED H U, HENRY A, et al. Genetic, physiological, and gene expression analyses reveal that multiple QTL enhance yield of rice mega-variety IR64 under drought[J]. PLoS One, 2013, 8(5): e62795. doi: 10.1371/journal.pone.0062795

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