Consensus genetic linkage map construction and QTL mapping for plant height-related traits in linseed flax (Linum usitatissimum L.)

Zhang, Jianping; Long, Yan; Wang, Liming; Dang, Zhao; Zhang, Tianbao; Song, Xiaxia; ZhanHai, Dang; Pei, Xinwu

doi:10.1186/s12870-018-1366-6

Cited by 30 publications

(34 citation statements)

References 41 publications

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“…Genetic antagonism effect between traits implies that some traits need to be "sacrificed" when some excellent phenotypes was artificially selected. Fiber flax breeding pays more attention to plant height because it is directly related to fiber yield (Zhang et al, 2018). Selection of plant height may result in small seed phenotypes being "bundled" together for artificial selection.…”

Section: Human-involved Selection Of Small Seeds During the Oil To Fimentioning

confidence: 99%

Resequencing 200 Flax Cultivated Accessions Identifies Candidate Genes Related to Seed Size and Weight and Reveals Signatures of Artificial Selection

et al. 2020

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Seed size and weight are key traits determining crop yield, which often undergo strongly artificial selection during crop domestication. Although seed sizes differ significantly between oil flax and fiber flax, the genetic basis of morphological differences and artificial selection characteristics in seed size remains largely unclear. Here we resequenced 200 flax cultivated accessions to generate a genome variation map based on chromosome assembly reference genomes. We provide evidence that oil flax group is the ancestor of cultivated flax, and the oil-fiber dual purpose group (OF) is the evolutionary intermediate transition state between oil and fiber flax. Genome-wide association studies (GWAS) were combined with LD Heatmap to identify candidate regions related to seed size and weight, then candidate genes were screened based on detailed functional annotations and estimation of nucleotide polymorphism effects. Using this strategy, we obtained 13 candidate genes related to seed size and weight. Selective sweeps analysis indicates human-involved selection of small seeds during the oil to fiber flax transition. Our study shows the existence of elite alleles for seed size and weight in flax germplasm and provides molecular insights into approaches for further improvement.

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Section: Human-involved Selection Of Small Seeds During the Oil To Fimentioning

confidence: 99%

Resequencing 200 Flax Cultivated Accessions Identifies Candidate Genes Related to Seed Size and Weight and Reveals Signatures of Artificial Selection

et al. 2020

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“…For the SNPs named based on the scaffold sequences, their scaffold names and coordinates were collected directly from the publications [17,26]. For the SNPs identified without a reference [18], flanking sequences of the SNP markers were downloaded from the publication [18]. All available primer sequences of SSR markers and flanking sequences of SNP markers for the identified QTL are listed in Tables S2 and S3, respectively.…”

Section: Marker Infomation Of Qtl In Flaxmentioning

confidence: 99%

“…For the SNPs identified without a reference sequence [18], the flanking sequences of the SNPs were searched against the RCPs using BLASTN at an E-value of 10 −30. The alignment regions of top hits were used and manually verified.…”

Section: Mapping Snps To the Most Recent Release Of The Chromosome-scmentioning

confidence: 99%

“…One QTL for branching score failed to map because its SSR marker Lu2067a could not be mapped to any region on the RCPs; this was likely because the marker was designed from a genotype different from the reference genome (cv CDC Bethune). Finally, the marker Lu8_185009 for QTL uq.C8-2 associated with plant height (PLH) and technical length (TL) [18] mapped to two different chromosomes (Chr 4 and Chr 7).…”

Section: Mapping Qtl Onto the Most Recent Release Of The Chromosome-smentioning

confidence: 99%

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Mapping Quantitative Trait Loci onto Chromosome-Scale Pseudomolecules in Flax

You

2020

MPs

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Quantitative trait loci (QTL) are genomic regions associated with phenotype variation of quantitative traits. To date, a total of 313 QTL for 31 quantitative traits have been reported in 14 studies on flax. Of these, 200 QTL from 12 studies were identified based on genetic maps, the scaffold sequences, or the pre-released chromosome-scale pseudomolecules. Molecular markers for QTL identification differed across studies but the most used ones were simple sequence repeats (SSRs) or single nucleotide polymorphisms (SNPs). To uniquely map the SSR and SNP markers from different references onto the recently released chromosome-scale pseudomolecules, methods with several scripts and database files were developed to locate PCR- and SNP-based markers onto the same reference, co-locate QTL, and scan genome-wide candidate genes. Using these methods, 195 out of 200 QTL were successfully sorted onto the 15 flax chromosomes and grouped into 133 co-located QTL clusters; the candidate genes that co-located with these QTL clusters were also predicted. The methods and tools presented in this article facilitate marker re-mapping to a new reference, genome-wide QTL analysis, candidate gene scanning, and breeding applications in flax and other crops.

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“…Phenotypic selection remains a major conventional breeding approach to improve traits of agronomic importance in flax. To accelerate the application of molecular breeding, a large number of molecular markers [11][12][13][14] and genetic populations [15][16][17][18] have been developed to assist QTL identification in the last decade. Using these genetic resources, a total of 267 QTL for 29 traits (11 seed yield and agronomic traits, 11 seed quality traits, four fibre traits, and three disease resistance traits) were reported in 13 studies (Tables 1 and 2).…”

mentioning

confidence: 99%

Mapping Quantitative Trait Loci onto Chromosome-scale Pseudomolecules in Flax

You

Cloutier

2019

Preprint

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Quantitative trait loci (QTL) are genomic regions associated with phenotype variation of quantitative traits in a population. To date, a total of 267 QTL for 29 quantitative traits have been reported in 13 studies on flax. Of these, 200 QTL from 12 studies were identified based on genetic maps, scaffold sequences, or pre-released chromosome-scale pseudomolecules. Molecular markers for QTL identification differed across studies but were mainly based on simple sequence repeat (SSR) or single nucleotide polymorphism (SNP) markers. This article provides methods with software tools and database files to uniquely map SSR and SNP markers from different references onto the recently released chromosome-scale pseudomolecules. Using these methods, 195 QTL were successfully sorted onto the 15 flax chromosomes and grouped into 133 co-located QTL clusters. Mapping of QTL from different studies to the same reference enables comparisons and facilitates genome-wide QTL analysis, candidate gene scanning, and breeding applications.

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Consensus genetic linkage map construction and QTL mapping for plant height-related traits in linseed flax (Linum usitatissimum L.)

Cited by 30 publications

References 41 publications

Resequencing 200 Flax Cultivated Accessions Identifies Candidate Genes Related to Seed Size and Weight and Reveals Signatures of Artificial Selection

Resequencing 200 Flax Cultivated Accessions Identifies Candidate Genes Related to Seed Size and Weight and Reveals Signatures of Artificial Selection

Mapping Quantitative Trait Loci onto Chromosome-Scale Pseudomolecules in Flax

Mapping Quantitative Trait Loci onto Chromosome-scale Pseudomolecules in Flax

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