AUTHOR=Dong Hongli , Tan Chuandong , Li Yuzhen , He Yan , Wei Shuai , Cui Yixin , Chen Yangui , Wei Dayong , Fu Ying , He Yajun , Wan Huafang , Liu Zhi , Xiong Qing , Lu Kun , Li Jiana , Qian Wei 

TITLE=Genome-Wide Association Study Reveals Both Overlapping and Independent Genetic Loci to Control Seed Weight and Silique Length in Brassica napus

JOURNAL=Frontiers in Plant Science

VOLUME=Volume 9 - 2018

YEAR=2018

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2018.00921

DOI=10.3389/fpls.2018.00921

ISSN=1664-462X

ABSTRACT=Seed weight (SW) is one of three determinants of seed yield, which positively correlates with the silique length (SL) in Brassica napus (rapeseed). However, the genetic mechanism underlying the relationship of two traits is largely unknown at present. A natural population comprised of 157 inbred lines in rapeseed was genotyped by whole-genome re-sequencing, and investigated for SW and SL over four years. The genome-wide association study identified 20 SNPs in significant association with SW on A01, A04, A09, C02 and C06 chromosomes and the phenotypic variation explained by a single locus ranged from 11.85% to 34.58%, with an average of 25.43%. Meanwhile, 742 SNPs significant associated with SL on A02, A03, A04, A07, A08, A09, C01, C03, C04, C06, C07 and C08 chromosomes were also detected and the phenotypic variation explained by a single locus ranged from 4.01% to 48.02%, with an average of 33.33%. Of which, more than half of loci were not been reported previously. There were 320 overlapped or linked SNPs for both SW and SL on A04, A09 and C06 chromosomes. It indicates that both overlapping and independent genetic loci controlled SW and SL in B. napus. On the haplotype block on A09, the allele variants of a known gene BnaA.ARF18.a controlling both SW and SL were identified in the natural population by developing derived cleaved amplified polymorphic sequence (dCAPS) markers. These findings are valuable for understanding the genetic mechanism of SW and SL and for further rapeseed molecular breeding programs.