Genome-Wide Analysis of Seed Acid Detergent Lignin (ADL) and Hull Content in Rapeseed (Brassica napus L.)

Abstract

A stable yellow-seeded variety is the breeding goal for obtaining the ideal rapeseed (Brassica napus L.) plant, and the amount of acid detergent lignin (ADL) in the seeds and the hull content (HC) are often used as yellow-seeded rapeseed screening indices. In this study, a genome-wide association analysis of 520 accessions was performed using the Q + K model with a total of 31,839 single-nucleotide polymorphism (SNP) sites. As a result, three significant associations on the B. napus chromosomes A05, A09, and C05 were detected for seed ADL content. The peak SNPs were within 9.27, 14.22, and 20.86 kb of the key genes BnaA.PAL4, BnaA.CAD2/BnaA.CAD3, and BnaC.CCR1, respectively. Further analyses were performed on the major locus of A05, which was also detected in the seed HC examination. A comparison of our genome-wide association study (GWAS) results and previous linkage mappings revealed a common chromosomal region on A09, which indicates that GWAS can be used as a powerful complementary strategy for dissecting complex traits in B. napus. Genomic selection (GS) utilizing the significant SNP markers based on the GWAS results exhibited increased predictive ability, indicating that the predictive ability of a given model can be substantially improved by using GWAS and GS.

Genome-wide association study and transcriptome analysis dissect the genetic control of silique length in Brassica napus L.

“…The genetic map that we developed earlier using a recombinant inbred line (RIL) mapping population with 172 lines was used for QTL mapping in this study [ 31 ]. A previously reported GWAS population with 520 accessions (referred to as the 60 K population) was used for association analysis of silique length [ 32 ], and another previously reported GWAS population with 588 accessions (referred to as the WGR population) was also used in this study [ 25 ]. There are 211 overlapping material between 60 K population and WGR population.…”

Expression Profile And Genome-Wide Association Analyze of Silique Length In Brassica Napus L.

“…The genetic map developed earlier by us using a recombinant inbred line (RIL) mapping population with 172 lines was used for QTL mapping in this study [29]. A previously reported GWAS population (referred to as 60K population) was used for association analysis of silique length [30], and another previously reported GWAS population (referred to as WGR population) was also used in this study [26]. The RILs population and the parents were grown in ve environments, winter of 2016, 2017, and 2018 in Southwest University in Beibei, Chongqing, China (cq; 29.80°N, 106.40°E), and summer of 2018 and 2019 in Xian, Shanxi, China (xa; 34.27°N, 108.08°E).…”

Inheritance of seed quality and seed germination in two doubled haploid populations of oilseed rape segregating for acid detergent lignin (ADL) content

“…Multiple genes and loci have been reported to be involved in the inheritance of seed coat color and testa thickness not only in Arabidopsis thaliana but also in Brassica species (e.g. Badani et al 2006;Stein et al 2013;Yan et al 2009;Liu et al 2015;Taylor-Teeples et al 2015;Wang et al 2015Wang et al , 2017Körber et al 2016).…”

“…In different populations a large number of QTL on linkage groups A05, A06, A09, C05, C08, C09, for reduced lignin content and yellow seed color have been published (Badani et al 2006;Stein et al 2013;Wang et al 2015Wang et al , 2017Behnke et al 2018;Miao et al 2019). Despite the identification of numerous loci affecting seed coat color in the allopolyploid genome of oilseed rape, none of the identified QTL have led to the development of competitive true yellow seeded rapeseed cultivars.…”