Dataset Information

Combined bulked segregant sequencing and traditional linkage analysis for identification of candidate gene for purple leaf sheath in maize.

ABSTRACT: Anthocyanin accumulation in various maize tissues plays important roles in plant growth and development. In addition, some color-related traits can be used as morphological markers in conventional maize breeding processes and purity identification of hybrid seeds. Here, we noticed that the leaf sheath color was controlled by a dominant gene, because purple (PSH) and green leaf sheaths (GSH) were separated at a ratio of 3:1 in an F2 population. To map the gene, an F2 and a recombinant inbred line (RIL) population were derived from a cross between inbred line T877 (PSH) and DH1M (GSH). The PSH locus was mapped to the genomic region within 128.8 to 138.4 Mb using a bulked segregant sequencing approach. This position was further validated by linkage mapping using 190 F2 plants with GSH. Subsequently, the PSH locus was fine-mapped into an interval of 304.2 kb. A maize gene, GRMZM5G822829, was identified in this region, encoding a bHLH transcription factor. The expression level of this gene in T877 was found to be 9-fold higher than that of DH1M. In conclusion, our results suggest that GRMZM5G822829 is the putative candidate gene conferring leaf sheath color in maize.

SUBMITTER: Li P

PROVIDER: S-EPMC5755806 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Combined bulked segregant sequencing and traditional linkage analysis for identification of candidate gene for purple leaf sheath in maize.

Li Pengcheng P Du Cancan C Zhang Yingying Y Yin Shuangyi S Zhang Enying E Fang Huimin H Lin Dezhou D Xu Chenwu C Yang Zefeng Z

PloS one 20180105 1

Anthocyanin accumulation in various maize tissues plays important roles in plant growth and development. In addition, some color-related traits can be used as morphological markers in conventional maize breeding processes and purity identification of hybrid seeds. Here, we noticed that the leaf sheath color was controlled by a dominant gene, because purple (PSH) and green leaf sheaths (GSH) were separated at a ratio of 3:1 in an F2 population. To map the gene, an F2 and a recombinant inbred line ...[more]

PMID: 29304111

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Project description:Waterlogging has increasingly become one of the major constraints to maize productivity in some maize production zones because it causes serious yield loss. Bulked segregant RNA-seq (BSR-seq) has been widely applied to profile candidate genes and map associated Single Nucleotide Polymorphism (SNP) markers in many species. In this study, 10 waterlogging sensitive and eight tolerant inbred lines were selected from 60 maize inbred lines with waterlogging response determined and preselected by the International Maize and Wheat Improvement Center (CIMMYT) from over 400 tropical maize inbred lines. BSR-seq was performed to identify differentially expressed genes and SNPs associated with waterlogging tolerance. Upon waterlogging stress, 354 and 1094 genes were differentially expressed in the tolerant and sensitive pools, respectively, compared to untreated controls. When tolerant and sensitive pools were compared, 593 genes were differentially expressed under untreated and 431 genes under waterlogged conditions, of which 122 genes overlapped. To validate the BSR-seq results, the expression levels of six genes were determined by qRT-PCR. The qRT-PCR results were consistent with BSR-seq results. Comparison of allelic polymorphism in mRNA sequences between tolerant and sensitive pools revealed 165 (normal condition) and 128 (waterlogged condition) high-probability SNPs. We found 18 overlapping SNPs with genomic positions mapped. Eighteen SNPs were contained in 18 genes, and eight and nine of 18 genes were responsive to waterlogging stress in tolerant and sensitive lines, respectively. Six alleles of the 18 originated from tolerant pool were significantly up-regulated under waterlogging, but not those from sensitive pool. Importantly, one allele (GRMZM2G055704) of the six genes was mapped between umc1619 and umc1948 on chromosome 1 where a QTL associated with waterlogging tolerance was identified in a previous research, strongly indicating that GRMZM2G055704 is a candidate gene responsive to waterlogging. Our research contributes to the knowledge of the molecular mechanism for waterlogging tolerance in maize.

Project description:BackgroundAnthocyanin accumulates in many plant tissues or organs, in rice for example leading to red, purple red and purple phenotypes for protection from damage by biotic and abiotic stresses and for reproduction. Purple leaf, leaf sheath, stigma, pericarp, and apiculus are common in wild rice and landraces and occasionally found in modern cultivars. No gene directly conferring anthocyanin deposited in a purple leaf sheath has yet been isolated by using natural variants. An F2 population derived from ssp. japonica cv. Tainung 72 (TNG72) with purple leaf sheath (PSH) crossed with ssp. indica cv. Taichung Sen 17 (TCS17) with green leaf sheath (GSH) was utilized to isolate a gene conferring leaf sheath color.ResultsBy positional cloning, 10-and 3-bp deletions in the R2R3 Myb domain of OsC1 were uncovered in GSH varieties TCS17 and Nipponbare, respectively. Allelic diversity, rather than gene expression levels of OsC1, might be responsible for anthocyanin accumulation. Parsimony-based analysis of genetic diversity in 50 accessions, including cultivars, landraces, and A-genome wild rice, suggests that independent mutation occurred in Asian, African, South American, and Australian species, while O. meridionalis had a divergent sequence. OsC1 was thought of as a domestication related gene, with up to 90 % reduction of genetic diversity in GSH; however, no values from three tests showed significant differences from neutral expectations, implying that OsC1 had not been subjected to recent selection. Haplotype network analysis revealed that species from different continents formed unique haplotypes with no gene flow. Two major groups of haplotypes corresponding to 10-bp deletion and other sequences were formed in Asian rice, including O. rufipogon, O. nivara and O. sativa. Introgressions of OsC1 between subspecies through natural and artificial hybridization were not rare. Because artificial and natural selection imposed admixture on rice germplasm in Taiwan, the genealogy of OsC1 might not be congruent with the current distribution of alleles through lineage diversification.ConclusionOsC1 is responsible for purple leaf sheath, and much new information about OsC1 is provided e.g., new alleles, non-domestication syndrome, and incongruence of genealogy with geographic distribution.

Dataset Information

Combined bulked segregant sequencing and traditional linkage analysis for identification of candidate gene for purple leaf sheath in maize.

Publications

Combined bulked segregant sequencing and traditional linkage analysis for identification of candidate gene for purple leaf sheath in maize.

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