A targeted QTL analysis for fiber length using a genetic population between two introgressed backcrossed inbred lines in upland cotton (Gossypium hirsutum)

Liu, Guoyuan; Pei, Wenfeng; Li, Dan; Ma, Jianjiang; Cui, Yupeng; Wang, Nuohan; Song, Jikun; Wu, Man; Li, Libei; Zang, Xinshan; Yu, Shuang; Zhang, Jinfa; Yu, Jie-Ae

doi:10.1016/j.cj.2018.11.005

Cited by 15 publications

(14 citation statements)

References 41 publications

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“…As a consequence, it has become a practical and convenient approach for genotyping in crop plants, 39-43 including the analysis of cotton for genetic diversity, genetic mapping and GWAS analysis. 44-47…”

Section: Discussionmentioning

confidence: 99%

Genotyping-by-Sequencing of Gossypium hirsutum Races and Cultivars Uncovers Novel Patterns of Genetic Relationships and Domestication Footprints

Zhang

Cai

Guo

et al. 2019

Evol Bioinform Online

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Determining the genetic rearrangement and domestication footprints in Gossypium hirsutum cultivars and primitive race genotypes are essential for effective gene conservation efforts and the development of advanced breeding molecular markers for marker-assisted breeding. In this study, 94 accessions representing the 7 primitive races of G hirsutum, along with 9 G hirsutum and 12 Gossypium barbadense cultivated accessions were evaluated. The genotyping-by-sequencing (GBS) approach was employed and 146 558 single nucleotide polymorphisms (SNP) were generated. Distinct SNP signatures were identified through the combination of selection scans and association analyses. Phylogenetic analyses were also conducted, and we concluded that the Latifolium, Richmondi, and Marie-Galante race accessions were more genetically related to the G hirsutum cultivars and tend to cluster together. Fifty-four outlier SNP loci were identified by selection-scan analysis, and 3 SNPs were located in genes related to the processes of plant responding to stress conditions and confirmed through further genome-wide signals of marker-phenotype association analysis, which indicate a clear selection signature for such trait. These results identified useful candidate gene locus for cotton breeding programs.

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Section: Discussionmentioning

confidence: 99%

Genotyping-by-Sequencing of Gossypium hirsutum Races and Cultivars Uncovers Novel Patterns of Genetic Relationships and Domestication Footprints

Zhang

Cai

Guo

et al. 2019

Evol Bioinform Online

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“…SNP markers with segregation patterns of ab × cd, ef × eg, hk × hk, nn × np, lm × ll in the parents were used to construct a linkage map. SNP markers with no more than 15% missing data in the F 1 population and a p -value of segregation distortion of less than 0.05 were selected to construct a linkage map ( Liu et al, 2019 ). The SNP markers were first divided into 38 groups according to the position mapped on the 38 chromosomes of the reference genome of “Yanjiang.” JoinMap 4.0 was used for the linkage map construction ( van Ooijen, 2006 ).…”

Section: Methodsmentioning

confidence: 99%

“…MareyMap was applied to construct a recombination map, which displayed a smooth curve with the Loess method ( Rezvoy et al, 2007 ). Regions no less than 50 cM/Mb were regarded as recombination hotspots ( Liu et al, 2019 ).…”

Section: Methodsmentioning

confidence: 99%

Identify of Fast-Growing Related Genes Especially in Height Growth by Combining QTL Analysis and Transcriptome in Salix matsudana (Koidz)

et al. 2021

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The study on the fast-growing traits of trees, mainly valued by tree height (TH) and diameter at breast height (DBH), is of great significance to promote the development of the forest industry. Quantitative trait locus (QTL) mapping based on high-density genetic maps is an efficient approach to identify genetic regions for fast-growing traits. In our study, a high-density genetic map for the F1 population was constructed. The genetic map had a total size of 5,484.07 centimorgan (cM), containing 5,956 single nucleotide polymorphisms (SNPs) based on Specific Length Amplified Fragment sequencing. Six fast-growing related stable QTL were identified on six chromosomes, and five stable QTL were identified by a principal component analysis (PCA). By combining the RNA-seq analysis for the two parents and two progenies with the qRT-PCR analysis, four candidate genes, annotated as DnaJ, 1-aminocyclopropane-1-carboxylate oxidase 1 (ACO1), Caffeic acid 3-O-methyltransferase 1 (COMT1), and Dirigent protein 6 (DIR6), that may regulate height growth were identified. Several lignin biosynthesis-related genes that may take part in height growth were detected. In addition, 21 hotspots in this population were found. The results of this study will provide an important foundation for further studies on the molecular and genetic regulation of TH and DBH.

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“…Most researchers have used these two software programs separately to carry out QTL mapping research on important cotton traits. For example, CIM was used by Li C. et al (2016) , Zhang et al (2016) and Liu et al (2018) , and ICIM was used by Liu et al (2017 , 2019 ) and Ma et al (2017) . However, these two mapping methods can be simultaneously used for locating QTLs to perform a more accurate and comprehensive genetic analysis of traits.…”

Section: Introductionmentioning

confidence: 99%

Quantitative Trait Locus Analysis and Identification of Candidate Genes for Micronaire in an Interspecific Backcross Inbred Line Population of Gossypium hirsutum × Gossypium barbadense

et al. 2021

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Cotton is the most important fiber crop and provides indispensable natural fibers for the textile industry. Micronaire (MIC) is determined by fiber fineness and maturity and is an important component of fiber quality. Gossypium barbadense L. possesses long, strong and fine fibers, while upland cotton (Gossypium hirsutum L.) is high yielding with high MIC and widely cultivated worldwide. To identify quantitative trait loci (QTLs) and candidate genes for MIC in G. barbadense, a population of 250 backcross inbred lines (BILs), developed from an interspecific cross of upland cotton CRI36 × Egyptian cotton (G. barbadense) Hai7124, was evaluated in 9 replicated field tests. Based on a high-density genetic map with 7709 genotyping-by-sequencing (GBS)-based single-nucleotide polymorphism (SNP) markers, 25 MIC QTLs were identified, including 12 previously described QTLs and 13 new QTLs. Importantly, two stable MIC QTLs (qMIC-D03-2 on D03 and qMIC-D08-1 on D08) were identified. Of a total of 338 genes identified within the two QTL regions, eight candidate genes with differential expression between TM-1 and Hai7124 were identified. Our research provides valuable information for improving MIC in cotton breeding.

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A targeted QTL analysis for fiber length using a genetic population between two introgressed backcrossed inbred lines in upland cotton (Gossypium hirsutum)

Cited by 15 publications

References 41 publications

Genotyping-by-Sequencing of Gossypium hirsutum Races and Cultivars Uncovers Novel Patterns of Genetic Relationships and Domestication Footprints

Genotyping-by-Sequencing of Gossypium hirsutum Races and Cultivars Uncovers Novel Patterns of Genetic Relationships and Domestication Footprints

Identify of Fast-Growing Related Genes Especially in Height Growth by Combining QTL Analysis and Transcriptome in Salix matsudana (Koidz)

Quantitative Trait Locus Analysis and Identification of Candidate Genes for Micronaire in an Interspecific Backcross Inbred Line Population of Gossypium hirsutum × Gossypium barbadense

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