Construction of a genetic map of rice RILs based on whole genome sequencing

WANG Chaohuan; SONG Bowen; YU Sijia; XIAO Wuming; HUANG Ming

doi:10.7671/j.issn.1001-411X.202006039

Journal of South China Agricultural University > 2021 > 42(2): 44-50. > DOI: 10.7671/j.issn.1001-411X.202006039

WANG Chaohuan, SONG Bowen, YU Sijia, et al. Construction of a genetic map of rice RILs based on whole genome sequencing[J]. Journal of South China Agricultural University, 2021, 42(2): 44-50. DOI: 10.7671/j.issn.1001-411X.202006039

Citation:

PDF (7792 KB)

Construction of a genetic map of rice RILs based on whole genome sequencing

College of Agriculture, South China Agricultural University/National Plant Breeding Engineering Technology Research center, Guangzhou 510642, China

More Information

Received Date: June 17, 2020
Available Online: May 17, 2023

Graphical Abstract

Abstract

Abstract

Objective
The indica cultivar ‘MDS’ and ‘R315’ were used as parents to construct a high-density genetic map, explore the important agronomic traits related genes of rice (Oryza sativa L.) and accelerate the breeding of rice cultivars.

Method
Whole genome sequencing of parents and their 192 recombinant inbred lines (RILs ) were performed to screen high-quality single nucleotide polymorphisms (SNPs) and construct bin markers. The bin markers were sorted using JoinMap4.0 for each linkage group, and perl SVG was used to draw the linkage map. Collinearity analysis was conducted according to the position of the markers on the genome and genetic map.

Result
A total of 221 494 high-quality SNPs were screened between the two parents. The constructed high-density genetic map contained 1 612 bin markers. The total map distance was 1 327.82 cM, and the average genetic map distance between adjacent markers was 0.82 cM. The collinearity analysis showed that the order of most markers on each linkage group was consistent with that on the genome. The collinearity was good and the map was of high quality.

Conclusion
The constructed high-density genetic map is of high quality, providing a preliminary basis for the subsequent identification of functional genes.
- Oryza sativa L.,
- recombinant inbred line,
- whole genome sequencing,
- genetic map

FullText(HTML)

References (19)

References

[1]	MCCOUCH S R, KOCHERT G, YU Z H, et al. Molecular mapping of rice chromosomes[J]. Theoretical and Applied Genetics, 1988, 76(6): 815-829. doi: 10.1007/BF00273666
[2]	徐建龙, 薛庆中, 罗利军, 等. 水稻单株有效穗数和每穗粒数的QTL剖析[J]. 遗传学报, 2001, 28(8): 752-759.
[3]	FOOLAD M R. Genome mapping and molecular breeding of tomato[J]. International Journal of Plant Genomics, 2007, 2007: 64358. doi: 10.1155/2007/64358.
[4]	LIU Z, ZHU H, LIU Y, et al. Construction of a high-density, high-quality genetic map of cultivated lotus (Nelumbo nucifera) using next-generation sequencing[J]. BMC Genomics, 2016, 17. doi: 10.1186/S12864-016-2781-4.
[5]	CHEN T X, ZHU Y J, CHEN K, et al. Identification of new QTL for salt tolerance from rice variety Pokkali[J]. Journal of Agronomy and Crop Science, 2020, 206(2): 202-213. doi: 10.1111/jac.12387
[6]	RAFALSKI A. Applications of single nucleotide polymorphisms in crop genetics[J]. Current Opinion in Plant Biology, 2002, 5(2): 94-100. doi: 10.1016/S1369-5266(02)00240-6
[7]	ALLEN G C, FLORES-VERGARA M A, KRASNYANSKI S, et al. A modified protocol for rapid DNA isolation from plant tissues using cetyltrimethylammonium bromide[J]. Nature Protocols, 2006, 1(5): 2320-2325. doi: 10.1038/nprot.2006.384
[8]	MCKENNA A, HANNA M, BANKS E, et al. The genome analysis toolkit: A mapreduce framework for analyzing next-generation DNA sequencing data[J]. Genome Research, 2010, 20(9): 1297-1303. doi: 10.1101/gr.107524.110
[9]	HUANG X, FENG Q, QIAN Q, et al. High-throughput genotyping by whole-genome resequencing[J]. Genome Research, 2009, 19(6): 1068-1076. doi: 10.1101/gr.089516.108
[10]	XUE W, XING Y, WENG X, et al. Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice[J]. Nature Genetics, 2008, 40(6): 761-767. doi: 10.1038/ng.143
[11]	ASHIKARI M. Cytokinin oxidase regulates rice grain production[J]. Science, 2005, 309(5735): 741-745. doi: 10.1126/science.1113373
[12]	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
[13]	WENG J, GU S, WAN X, et al. Isolation and initial characterization of GW5, a major QTL associated with rice grain width and weight[J]. Cell Research, 2008, 18(12): 1199-1209. doi: 10.1038/cr.2008.307
[14]	FAN C, XING Y, MAO H, et al. GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein[J]. Theoretical and Applied Genetics, 2006, 112(6): 1164-1171. doi: 10.1007/s00122-006-0218-1
[15]	WANG S, WU K, YUAN Q, et al. Control of grain size, shape and quality by OsSPL16 in rice[J]. Genome Research, 2012, 44(8): 950-955.
[16]	WU Y, WANG Y, MI X, et al. The QTL GNP1 encodes GA20ox1, which increases grain number and yield by increasing cytokinin activity in rice panicle meristems[J]. PLoS Genetics, 2016, 12(10): e1006386. doi: 10.1371/journal.pgen.1006386
[17]	JANSEN R C. Studying complex biological systems using multifactorial perturbation[J]. Nature Reviews Genetics, 2003, 4(2): 145-151. doi: 10.1038/nrg996
[18]	王英. 利用回交导入系筛选水稻高产、抗旱和耐盐株系及选择导入系相关性状的QTL定位[D]. 北京: 中国农业科学院, 2013.
[19]	冯博. 水稻抗旱和耐低氮QTL定位及优异等位基因的聚合效应评价[D]. 沈阳: 沈阳农业大学, 2018.

Cited By

Cited by

Periodical cited type(3)

1.	国显宝，韩冰，逯新民，何奕成，于露，张万通，段丽辉，耿依仪，邵新庆，俞点，韩伽怡. 氮添加对青藏高原高寒草甸丛枝菌根真菌群落的影响. 草地学报. 2024(07): 2054-2061 .
2.	薛壮壮，冯童禹，王超，沈仁芳. 磷肥对酸性红壤上玉米不同部位丛枝菌根真菌群落的影响. 土壤. 2023(05): 1008-1015 .
3.	胡家欣，彭思利，张栋，葛之葳，杨楠. 氮添加对不同林龄杨树人工林丛枝菌根真菌群落的影响. 生态环境学报. 2020(09): 1768-1775 .

Other cited types(10)

Get Citation

PDF

XML

Article views (1218) PDF downloads (1717) Cited by(13)

Turn off MathJax

Article Contents

Abstract

References

Construction of a genetic map of rice RILs based on whole genome sequencing

Abstract

References

Cited by

Periodical cited type(3)

Other cited types(10)

Catalog

Export File

Citation

Format

Content