2016
DOI: 10.1038/ng.3634
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Subgenome parallel selection is associated with morphotype diversification and convergent crop domestication in Brassica rapa and Brassica oleracea

Abstract: Brassica species, including crops such as cabbage, turnip and oilseed, display enormous phenotypic variation. Brassica genomes have all undergone a whole-genome triplication (WGT) event with unknown effects on phenotype diversification. We resequenced 199 Brassica rapa and 119 Brassica oleracea accessions representing various morphotypes and identified signals of selection at the mesohexaploid subgenome level. For cabbage morphotypes with their typical leaf-heading trait, we identified four subgenome loci that… Show more

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Cited by 315 publications
(390 citation statements)
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“…Finally, we called out 2,249,473 and 3,852,169 reliable SNPs (single-nucleotide polymorphisms), as well as 303,617 and 417,004 InDels for the B. rapa and B. oleracea populations, respectively. With these datasets, we have identified genomic selection signals for traits of leaf-heading and tuberous organs in both B. rapa and B. oleracea , and found that sub-genome parallel selection was associated with morphotype diversification and convergent crop domestication in the two Brassica species 21 .…”
Section: Background and Summarymentioning
confidence: 99%
“…Finally, we called out 2,249,473 and 3,852,169 reliable SNPs (single-nucleotide polymorphisms), as well as 303,617 and 417,004 InDels for the B. rapa and B. oleracea populations, respectively. With these datasets, we have identified genomic selection signals for traits of leaf-heading and tuberous organs in both B. rapa and B. oleracea , and found that sub-genome parallel selection was associated with morphotype diversification and convergent crop domestication in the two Brassica species 21 .…”
Section: Background and Summarymentioning
confidence: 99%
“…More recent studies have capitalized on whole-genome sequencing and single nucleotide polymorphism (SNP) genotyping approaches such as amplicon sequencing (AmpSeq) and genotyping-by-sequencing (GBS) (Cheng et al, 2016a,b; Tanhuanpää et al, 2016). …”
Section: Introductionmentioning
confidence: 99%
“…Recently, using 209 SNPs, Tanhuanpää et al (2016) identified three main groups related to morphotype and flowering habit of 61 accessions. Furthermore, the populations used in the studies of Guo et al (2014), Zhao et al (2005, 2007, 2010), Del Carpio et al (2011a,b), Dixon (2007), Tanhuanpää et al (2016), and Cheng et al (2016a,b) suffer from little (one to two accessions) or no representation of subspecies such as ssp. dichotoma and ssp.…”
Section: Introductionmentioning
confidence: 99%
“…However, the AMT2 subfamily in A. thaliana has only one member, while there are two members in B. campestris and B. rapa. Brassica plants have all undergone a whole-genome triplication event (Cheng et al 2013) that might have originated the three paleo-subgenomes and multiple copies of paralogous genes found in the genomes of B. rapa and B. oleracea (Cheng et al 2016), as observed for PtrAMT2;1 and PtrAMT2;2 (Couturier et al 2007). Duplicate genes can potentially diverge in their roles as well as retain different sub-function of the original gene.…”
mentioning
confidence: 99%