Identification of QTL related to anther color and hull color by RAD sequencing in a RIL population of Setaria italica

Xie, Huifang; Hou, Junliang; Fu, Nan; Wei, Menghan; Li, Yunfei; Yu, Kun; Song, Hui; Li, Shiming; Liu, Jinrong

doi:10.1186/s12864-021-07882-x

Cited by 7 publications

(11 citation statements)

References 60 publications

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“…Sihc1 was discovered at the end of chromosome 6 based on ndings from two preceding studies.However, these speci c QTLs did not align with the QTLs identi ed in this study. In our study, two QTLs namely, qHC1.1 and qHC1.2 were found to be in agreement with qHC1 and qHC2 previously reported by Xie et al(Xie et al 2021). Interestingly, both this study and the previous publication used RILs derived from Yugu 18 × Hongjiugu crosses and constructed a high-density bin map for QTL mapping.…”

supporting

confidence: 92%

“…Through linkage analysis and genomewide association study, QTLs were identi ed on chromosomes 1, 2, 3, 6, 7, and 9. Additionally, 11 potential candidate genes were identi ed on chromosomes 1, 6 and 9 (Seita.1G057300, Si1g06530, Seita.1G057100, Seita.1G059100, Seita.1G059300, Seita.6G226500, Seita.6G226800, Seita.6G228300, Seita.6G228600, Seita.9G515900 and Seita.9G515900) (Guo et Xie et al 2021). Sihc1 on chromosome 6 has been consistently identi ed in linkage analysis and genome-wide association studies (Jia et al 2013;Wang et al 2017).…”

Section: Introductionmentioning

confidence: 99%

“…Xie et al 2021), cucumber(Kishor et al 2021), wheat(Lin et al 2016), and other plants.Xie et al classi ed the hull color in foxtail millet into two categories, red and golden yellow, using Method I for QTL detection(Xie et al 2021). Method II is a more detailed identi cation of hull color relative to Method I.…”

mentioning

confidence: 99%

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Identification and candidate gene screening of qHC1.2 , a Major QTL associated with hull color in foxtail millet ( Setaria italica L.)

Chai,

Yang,

Shi

et al. 2023

Preprint

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Hull color is a crucial characteristic that helps assess the nutritional value and economic potential of foxtail millet. However, the reports on quantitative trait locus (QTL) mapping and map-based cloning for hull color are limited. Here, we mapped QTLs responsible for hull color by using 215 recombinant inbred lines (RILs) derived from Yugu 18 (Light yellow hull) × Hongjiugu (Red hull) and a high-density bin map. A total of 36 QTLs for hull color were detected in all four environments by four phenotypic evaluation methods. Among these QTLs, a major QTL for hull color (HC) named qHC1.2 was repeatedly mapped on chromosome 1 and explained 8.89 – 69.63% of the phenotypic variation. In addition, RNA sequencing (RNA-seq) was performed 7, 14, and 21 days after flowering for the YRRIL-145 and YRRIL-229, and three differentially expressed genes (DEGs) were detected in the candidate region. The qRT-PCR results showed the same expression patterns as the RNA-seq data. Among them, DEGs, only one gene, Seita.1G057300, encoding a cinnamyl alcohol dehydrogenase (CAD), was located in the candidate region of qHC1.2. Furthermore, sequence analysis revealed One SNP (A to G), located at the third exon, resulted in an amino acid change from isoleucine to valine in YRRIL-145 compared with YRRIL-229. Our results provide a foundation for further cloning of qHC1.2 and will be very useful in clarifying the regulatory mechanism for hull color synthesis in foxtail millet.

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confidence: 92%

Section: Introductionmentioning

confidence: 99%

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Identification and candidate gene screening of qHC1.2 , a Major QTL associated with hull color in foxtail millet ( Setaria italica L.)

Chai,

Yang,

Shi

et al. 2023

Preprint

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“…The data that are obtained by RAD not only have the advantages of being convenient and highly reproducible, but also, they can be accurately located in the genome position for more applications. For example, the candidate genes with known functions can be identified by annotating the outlier loci through the selection elimination analysis [ 53 , 54 ]. At the same time, the SNPs that are obtained by RAD-seq can provide more accurate and reliable information for a genetic and evolutionary analysis.…”

Section: Discussionmentioning

confidence: 99%

Population Diversity Analysis Provide Insights into Provenance Identification of Dendrobium catenatum

Zheng

et al. 2022

Genes

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Dendrobium catenatum (Dendrobium officinale) is a valuable genuine herb. The source of this species is difficult to be identified by traditional methods including morphology, spectroscopy, and chromatography. We used the restriction site-associated DNA sequencing (RAD-seq) approach to perform the high-throughput sequencing of 24 D. catenatum provenances. In this study, 371.18 Gb clean data were obtained, and 655,057 high-quality SNPs were selected after their filtration. We used phylogenetic tree, genetic structure, and principal component analyses to examine the genetic diversities and genetic relationships of the 109 accessions. We found that D. catenatum could be divided into two groups, and each group was closely related to the distribution of the sampling sites. At the population level, the average nucleotide diversity (π) of the D. catenatum population mutation parameters was 0.1584 and the expected heterozygosity (HE) was 0.1575. The GXLPTP07 accessions showed the highest genetic diversity in terms of the private allele number, observed heterozygosity, and nucleotide diversity. The Mantel test showed a significant positive correlation between the genetic and geographic distances among the overall distribution. A genetic information database of D. catenatum was established, which confirmed that RAD-seq technology has the potential to be applied in the identification of medicinal Dendrobium of different origins.

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“…Beauv.) is an important reserve cereal crop that is rich in proteins, vitamins, fatty acids, amino acids, and dietary fibers [ 1 , 2 ]. Due to its unique nutritional and medicinal properties, the demand for foxtail millet has increased in recent years [ 3 ].…”

Section: Introductionmentioning

confidence: 99%

Mapping of major QTL and candidate gene analysis for hull colour in foxtail millet (Setaria italica (L.) P. Beauv.)

et al. 2023

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Background Hull colour is an important morphological marker for selection in seed production of foxtail millet. However, the molecular mechanisms underlying hull colour variation remain unknown. Results An F7 recombinant inbred line (RIL) population containing 215 lines derived from Hongjiugu × Yugu18 was used to analyze inheritance and detect the quantitative trait loci (QTL) for four hull colour traits using major gene plus polygene mixed inheritance analysis and composite interval mapping (CIM) in four environments. Genetic analysis revealed that the hull colour L* value (HCL*) was controlled by two major genes plus additive polygenes, the hull colour a* value (HCa*) was controlled by three major genes, the hull colour b* value (HCb*) was controlled by two major genes plus polygenes, and the hull colour C* value (HCC*) was controlled by four major genes. A high-density genetic linkage map covering 1227.383 cM of the foxtail millet genome, with an average interval of 0.879 cM between adjacent bin markers, was constructed using 1420 bin markers. Based on the genetic linkage map and the phenotypic data, a total of 39 QTL were detected for these four hull colour traits across four environments, each explaining 1.50%–49.20% of the phenotypic variation. Of these, six environmentally stable major QTL were co-localized to regions on chromosomes 1 and 9, playing a major role in hull colour. There were 556 annotated genes within the two QTL regions. Based on the functions of homologous genes in Arabidopsis and the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) gene annotations, five genes were predicted as candidate genes for further studies. Conclusions This is the first study to use an inheritance model and QTL mapping to determine the genetic mechanisms of hull colour trait in foxtail millet. We identified six major environmentally stable QTL and predicted five potential candidate genes to be associated with hull colour. These results advance the current understanding of the genetic mechanisms underlying hull colour traits in foxtail millet and provide additional resources for application in genomics-assisted breeding and potential isolation and functional characterization of the candidate genes.

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Identification of QTL related to anther color and hull color by RAD sequencing in a RIL population of Setaria italica

Cited by 7 publications

References 60 publications

Identification and candidate gene screening of qHC1.2 , a Major QTL associated with hull color in foxtail millet ( Setaria italica L.)

Identification and candidate gene screening of qHC1.2 , a Major QTL associated with hull color in foxtail millet ( Setaria italica L.)

Population Diversity Analysis Provide Insights into Provenance Identification of Dendrobium catenatum

Mapping of major QTL and candidate gene analysis for hull colour in foxtail millet (Setaria italica (L.) P. Beauv.)

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