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Exploring the genetic characteristics of two recombinant inbred line populations via high-density SNP markers in maize.

ABSTRACT: Understanding genetic characteristics can reveal the genetic diversity in maize and be used to explore evolutionary mechanisms and gene cloning. A high-density linkage map was constructed to determine recombination rates (RRs), segregation distortion regions (SDRs), and recombinant blocks (RBs) in two recombinant inbred line populations (RILs) (B73/By804 and Zong3/87-1) generated by the single seed descent method. Population B73/By804 containing 174 lines were genotyped with 198 simple sequence repeats (SSRs) markers while population Zong3/87-1 comprised of 175 lines, were genotyped with 210 SSR markers along with 1536 single nucleotide polymorphism (SNP) markers for each population, spanning 1526.7 cM and 1996.2 cM in the B73/By804 and Zong3/87-1 populations, respectively. The total variance of the RR in the whole genome was nearly 100 fold, and the maximum average was 10.43-11.50 cM/Mb while the minimum was 0.08-0.10 cM/Mb in the two populations. The average number of RB was 44 and 37 in the Zong3/87-1 and B73/By804 populations, respectively, whereas 28 SDRs were observed in both populations. We investigated 11 traits in Zong3/87-1 and 10 traits in B73/By804. Quantitative trait locus (QTLs) mapping of SNP+SSR with SNP and SSR marker sets were compared to showed the impact of different density markers on QTL mapping and resolution. The confidence interval of QTL Pa19 (FatB gene controlling palmitic acid content) was reduced from 3.5 Mb to 1.72 Mb, and the QTL Oil6 (DGAT1-2 gene controlling oil concentration) was significantly reduced from 10.8 Mb to 1.62 Mb. Thus, the use of high-density markers considerably improved QTL mapping resolution. The genetic information resulting from this study will support forthcoming efforts to understand recombination events, SDRs, and variations among different germplasm. Furthermore, this study will facilitate gene cloning and understanding of the fundamental sources of total variation and RR in maize, which is the most widely cultivated cereal crop.

SUBMITTER: Pan Q

PROVIDER: S-EPMC3531342 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

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Exploring the genetic characteristics of two recombinant inbred line populations via high-density SNP markers in maize.

Pan Qingchun Q Ali Farhan F Yang Xiaohong X Li Jiansheng J Yan Jianbing J

PloS one 20121227 12

Understanding genetic characteristics can reveal the genetic diversity in maize and be used to explore evolutionary mechanisms and gene cloning. A high-density linkage map was constructed to determine recombination rates (RRs), segregation distortion regions (SDRs), and recombinant blocks (RBs) in two recombinant inbred line populations (RILs) (B73/By804 and Zong3/87-1) generated by the single seed descent method. Population B73/By804 containing 174 lines were genotyped with 198 simple sequence ...[more]

PMID: 23300772

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Project description:BackgroundMaize (Zea mays ssp. mays) is the most abundantly cultivated and highly valued food commodity in the world. Oil from maize kernels is highly nutritious and important for the diet and health of humans, and it can be used as a source of bioenergy. A better understanding of genetic basis for maize kernel oil can help improve the oil content and quality when applied in breeding.ResultsIn this study, a KUI3/SC55 recombinant inbred line (RIL) population, consisting of 180 individuals was constructed from a cross between inbred lines KUI3 and SC55. We phenotyped 19 oil-related traits and subsequently dissected the genetic architecture of oil-related traits in maize kernels based on a high-density genetic map. In total, 62 quantitative trait loci (QTLs), with 2 to 5 QTLs per trait, were detected in the KUI3/SC55 RIL population. Each QTL accounted for 6.7% (qSTOL1) to 31.02% (qBELI6) of phenotypic variation and the total phenotypic variation explained (PVE) of all detected QTLs for each trait ranged from 12.5% (OIL) to 52.5% (C16:0/C16:1). Of all these identified QTLs, only 5 were major QTLs located in three genomic regions on chromosome 6 and 9. In addition, two pairs of epistatic QTLs with additive effects were detected and they explained 3.3 and 2.4% of the phenotypic variation, respectively. Colocalization with a previous GWAS on oil-related traits, identified 19 genes. Of these genes, two important candidate genes, GRMZM2G101515 and GRMZM2G022558, were further verified to be associated with C20:0/C22:0 and C18:0/C20:0, respectively, according to a gene-based association analysis. The first gene encodes a kinase-related protein with unknown function, while the second gene encodes fatty acid elongase 2 (fae2) and directly participates in the biosynthesis of very long chain fatty acids in Arabidopsis.ConclusionsOur results provide insights on the genetic basis of oil-related traits and a theoretical basis for improving maize quality by marker-assisted selection.

Project description:BackgroundMaize (Zea Mays L.) is one of the most important cereal crops worldwide and provides food for billions of people. Stalk lodging can greatly undermine the standability of maize plants and therefore decrease crop yields. Rind penetrometer resistance is an effective and reliable method for evaluating maize stalk strength, which is highly correlated with stalk lodging resistance. In this study, two recombinant inbred line populations were constructed from crosses between the H127R and Chang7-2 lines, and between the B73 and By804 lines. We genotyped these two populations and their parents using 3,072 single nucleotide polymorphism markers and performed phenotypic assessment of rind penetrometer resistance in multiple environments to dissect the genetic architecture of rind penetrometer resistance in maize.ResultsBased on two linkage maps of 1,397.1 and 1,600.4 cM with average interval of 1.7 and 2.1 cM between adjacent makers, respectively, seven quantitative trait loci (QTL) for rind penetrometer resistance were detected in the two recombinant inbred line populations. These QTL were distributed in seven genomic regions, and each accounted for 4.4-18.9% of the rind penetrometer resistance variation. The QTL with the largest effect on rind penetrometer resistance, qRPR3-1, was located on chromosome 3 with the flanking markers PZE-103123325 and SYN23245. This locus was further narrowed down to a 3.1-Mb interval by haplotype analysis using high-density markers in the target region. Within this interval, four genes associated with the biosynthesis of cell wall components were considered as potential candidate genes for the rind penetrometer resistance effect.ConclusionsThe inheritance of rind penetrometer resistance is rather complex. A few large-effect quantitative trait loci, together with a several minor-effect QTL, contributed to the phenotypic variation in rind penetrometer resistance in the two recombinant inbred line populations that were examined. A potential approach for improving stalk strength and crop yields in commercial maize lines may be to introgress favorable alleles of the locus that was found to have the largest effect on rind penetrometer resistance (qRPR3-1).

Dataset Information

Exploring the genetic characteristics of two recombinant inbred line populations via high-density SNP markers in maize.

Publications

Exploring the genetic characteristics of two recombinant inbred line populations via high-density SNP markers in maize.

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