Joint QTL mapping and transcriptome sequencing analysis reveal candidate flowering time genes in Brassica napus L

Jian, Hongju; Zhang, Aoxiang; Ma, Jinqi; Wang, Tengyue; Yang, Bo; Shuang, Lan Shuan; Liu, Min; Li, Jiana; Xu, Xinhua; Paterson, Andrew H.; Liu, Liezhao

doi:10.1186/s12864-018-5356-8

Cited by 52 publications

(54 citation statements)

References 72 publications

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“…One of these nine genes was subsequently functionally validated [32]. Similar combinatorial approaches have been applied to identify key candidate genes responsible for variation in salt tolerance in rice ( Oryza rufipogon ) [197] and flowering time in rape ( Brassica napus ) [198]. Population genetics data that provides genome wide insights into signatures of selection can equally be combined with comparative expression data to reveal meaningful candidate genes underlying divergence of relevant phenotypic traits [199].…”

Section: Discussionmentioning

confidence: 99%

Cloudy with a Chance of Insights: Context Dependent Gene Regulation and Implications for Evolutionary Studies

Buchberger

Reis

et al. 2019

Genes

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Research in various fields of evolutionary biology has shown that divergence in gene expression is a key driver for phenotypic evolution. An exceptional contribution of cis-regulatory divergence has been found to contribute to morphological diversification. In the light of these findings, the analysis of genome-wide expression data has become one of the central tools to link genotype and phenotype information on a more mechanistic level. However, in many studies, especially if general conclusions are drawn from such data, a key feature of gene regulation is often neglected. With our article, we want to raise awareness that gene regulation and thus gene expression is highly context dependent. Genes show tissue- and stage-specific expression. We argue that the regulatory context must be considered in comparative expression studies.

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Section: Discussionmentioning

confidence: 99%

Cloudy with a Chance of Insights: Context Dependent Gene Regulation and Implications for Evolutionary Studies

Buchberger

Reis

et al. 2019

Genes

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“…This notion indicates that QTL mapping analysis of complex quantitative traits in alfalfa could be challenging and that large populations will be needed [33]. Compared with other QTL mapping populations in alfalfa [12,17] and other species [34,35], the population in our study was sufficiently large for the QTL mapping of spring regrowth vigor traits.…”

Section: Discussionmentioning

confidence: 95%

Detection of Quantitative Trait Loci (QTL) associated with the spring regrowth vigor trait in alfalfa (Medicago sativa L.)

Jiang

Zhang

Zhen

et al. 2020

Preprint

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Background: Alfalfa ( Medicago sativa L.) is a perennial forage legume with a reputation as being the "queen of forage". Spring regrowth vigor refers to the process of perennial alfalfa returning to growth after winter survival. The objective of this research was to identify candidate genes significantly associated with spring regrowth vigor.Results: We used a tetraploid alfalfa F1 population comprised of 392 progenies to identify quantitative trait loci (QTL) that control this trait. The F1 population phenotypic data were collected using a total of three environmental phenotypic data. The mapping population was genotyped using Genotyping-bysequencing (GBS), and linkage maps were developed based on single nucleotide polymorphism (SNP) markers. Fifteen significant QTL for spring regrowth vigor were detected in both parents. Five QTL were identified in the male genetic map, while ten QTL were identified in the female. Four QTL were located on homolog 7D of the male parent, and two QTL were colocalized. Five QTL were mapped on homolog 6D of the female parent, and two QTL were colocalized.Conclusions: The QTL presented in this study can be used to improve the efficiency of alfalfa breeding programs and provide valuable resources for the genetic improvement of alfalfa using markerassisted selection (MAS). β These authors contributed equally to this research. Background Alfalfa (Medicago sativa L.) is a high-value autotetraploid (2n = 4 × = 32) legume forage crop with a genome size of approximately 1000 Mb [1, 2], and has a very wide range of uses, such as in hay, silage and pasture [3]. Alfalfa plants are highly heterozygous and exhibit severe inbreeding depression, precluding the development of inbred lines [4]. Alfalfa breeding programs have focused on forage yield, quality, fall dormancy and resistance to biotic and abiotic stressors. Conventional breeding programs are usually based on simple phenotypic selection, which requires a long breeding

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“…Subsequent functional validation tests confirmed the involvement of one of the candidates in the respective behavioral differences [32]. Similar combinations of QTL mapping and genome wide differential expression analyses have been applied to identify key candidate genes responsible for variation in salt tolerance in rice (Oryza rufipogon) [162] and flowering time in rape (Brassica napus) [163].…”

Section: Impact Of Tissue-specificity On Signal-to-noise Ratiomentioning

confidence: 92%

Cloudy with a Chance of Insights: Context Dependent Gene Regulation and Implications for the Evolution of Gene Expression

Buchberger¹,

Reis²,

Lu³

et al. 2019

Preprint

View full text Add to dashboard Cite

Research in various fields of evolutionary biology has shown that divergence in gene expression is a key driver for phenotypic variation. An exceptional contribution of cis-regulatory evolution has for instance been found to contribute to morphological diversification. In the light of these findings, the analysis of genome-wide expression data has become one of the central tools to link genotype and phenotype information on a more mechanistic level. However, in many studies, especially if general conclusions are drawn from such data, a key feature of gene regulation is often neglected. With our article, we want to raise awareness that gene regulation and thus gene expression is highly context dependent. Genes show tissue- and developmental stage-specific expression. We argue that the regulatory context must be considered when studying evolution of gene expression.

show abstract

Joint QTL mapping and transcriptome sequencing analysis reveal candidate flowering time genes in Brassica napus L

Cited by 52 publications

References 72 publications

Cloudy with a Chance of Insights: Context Dependent Gene Regulation and Implications for Evolutionary Studies

Cloudy with a Chance of Insights: Context Dependent Gene Regulation and Implications for Evolutionary Studies

Detection of Quantitative Trait Loci (QTL) associated with the spring regrowth vigor trait in alfalfa (Medicago sativa L.)

Cloudy with a Chance of Insights: Context Dependent Gene Regulation and Implications for the Evolution of Gene Expression

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