Dataset Information

Construction of the third-generation Zea mays haplotype map.

ABSTRACT: Background:Characterization of genetic variations in maize has been challenging, mainly due to deterioration of collinearity between individual genomes in the species. An international consortium of maize research groups combined resources to develop the maize haplotype version 3 (HapMap 3), built from whole-genome sequencing data from 1218 maize lines, covering predomestication and domesticated Zea mays varieties across the world. Results:A new computational pipeline was set up to process more than 12 trillion bp of sequencing data, and a set of population genetics filters was applied to identify more than 83 million variant sites. Conclusions:We identified polymorphisms in regions where collinearity is largely preserved in the maize species. However, the fact that the B73 genome used as the reference only represents a fraction of all haplotypes is still an important limiting factor.

SUBMITTER: Bukowski R

PROVIDER: S-EPMC5890452 | biostudies-literature | 2018 Apr

REPOSITORIES: biostudies-literature

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Construction of the third-generation Zea mays haplotype map.

Bukowski Robert R Guo Xiaosen X Lu Yanli Y Zou Cheng C He Bing B Rong Zhengqin Z Wang Bo B Xu Dawen D Yang Bicheng B Xie Chuanxiao C Fan Longjiang L Gao Shibin S Xu Xun X Zhang Gengyun G Li Yingrui Y Jiao Yinping Y Doebley John F JF Ross-Ibarra Jeffrey J Lorant Anne A Buffalo Vince V Romay M Cinta MC Buckler Edward S ES Ware Doreen D Lai Jinsheng J Sun Qi Q Xu Yunbi Y

GigaScience 20180401 4

<h4>Background</h4>Characterization of genetic variations in maize has been challenging, mainly due to deterioration of collinearity between individual genomes in the species. An international consortium of maize research groups combined resources to develop the maize haplotype version 3 (HapMap 3), built from whole-genome sequencing data from 1218 maize lines, covering predomestication and domesticated Zea mays varieties across the world.<h4>Results</h4>A new computational pipeline was set up t ...[more]

PMID: 29300887

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Project description:Increasing grain yield is the ultimate goal for maize breeding. High resolution quantitative trait loci (QTL) mapping can help us understand the molecular basis of phenotypic variation of yield and thus facilitate marker assisted breeding. The aim of this study is to use genotyping-by-sequencing (GBS) for large-scale SNP discovery and simultaneous genotyping of all F2 individuals from a cross between two varieties of maize that are in clear contrast in yield and related traits. A set of 199 F2 progeny derived from the cross of varieties SG-5 and SG-7 were generated and genotyped by GBS. A total of 1,046,524,604 reads with an average of 5,258,918 reads per F2 individual were generated. This number of reads represents an approximately 0.36-fold coverage of the maize reference genome Zea_mays.AGPv3.29 for each F2 individual. A total of 68,882 raw SNPs were discovered in the F2 population, which, after stringent filtering, led to a total of 29,927 high quality SNPs. Comparative analysis using these physically mapped marker loci revealed a higher degree of synteny with the reference genome. The SNP genotype data were utilized to construct an intra-specific genetic linkage map of maize consisting of 3,305 bins on 10 linkage groups spanning 2,236.66 cM at an average distance of 0.68 cM between consecutive markers. From this map, we identified 28 QTLs associated with yield traits (100-kernel weight, ear length, ear diameter, cob diameter, kernel row number, corn grains per row, ear weight, and grain weight per plant) using the composite interval mapping (CIM) method and 29 QTLs using the least absolute shrinkage selection operator (LASSO) method. QTLs identified by the CIM method account for 6.4% to 19.7% of the phenotypic variation. Small intervals of three QTLs (qCGR-1, qKW-2, and qGWP-4) contain several genes, including one gene (GRMZM2G139872) encoding the F-box protein, three genes (GRMZM2G180811, GRMZM5G828139, and GRMZM5G873194) encoding the WD40-repeat protein, and one gene (GRMZM2G019183) encoding the UDP-Glycosyltransferase. The work will not only help to understand the mechanisms that control yield traits of maize, but also provide a basis for marker-assisted selection and map-based cloning in further studies.

Dataset Information

Construction of the third-generation Zea mays haplotype map.

Publications

Construction of the third-generation Zea mays haplotype map.

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