Genome-wide association mapping unravels the genetic control of seed germination and vigor in Brassica napus

Abstract

Rapid and uniform seed germination is a crucial prerequisite for crop establishment and high yield levels in crop production. A disclosure of genetic factors contributing to adequate seed vigor would help to further increase yield potential and stability. Here we carried out a genome-wide association study in order to define genomic regions influencing seed germination and early seedling growth in oilseed rape (Brassica napus L.). A population of 248 genetically diverse winter-type B. napus accessions was genotyped with the Brassica 60k SNP Illumina genotyping array. Automated high-throughput in vitro phenotyping provided extensive data for multiple traits related to germination and early vigor, such as germination speed, absolute germination rate and radicle elongation. The data obtained indicate that seed germination and radicle growth are strongly environmentally dependent, but could nevertheless be substantially improved by genomic-based breeding. Conditions during seed production and storage were shown to have a profound effect on seed vigor, and a variable manifestation of seed dormancy appears to contribute to differences in germination performance in B. napus. Several promising positional and functional candidate genes could be identified within the genomic regions associated with germination speed, absolute germination rate, radicle growth and thousand seed weight. These include B. napus orthologs of the Arabidopsis thaliana genes SNOWY COTYLEDON 1 (SCO1), ARABIDOPSIS TWO-COMPONENT RESPONSE REGULATOR (ARR4), and ARGINYL-t-RNA PROTEIN TRANSFERASE 1 (ATE1), which have been shown previously to play a role in seed germination and seedling growth in A. thaliana.

Genome-wide association-mapping for fruit quality traits in tomato

“…It can be first used to detect the preliminary locations of QTLs to study the mechanisms underlying phenotypic variation, and then to use linkage analysis for more precise location of those QTLs that are of special interest (Mazzucato et al 2008;Atwell et al 2010;Xu et al 2013). Since the first use to dissect candidate genes on inbred maize lines (Thornsberry et al 2001), GWAS analyses have been widely constructed on a number of major plant species (Ruggieri et al 2014;Wen et al 2014;Hatzig et al 2015;Kumar et al 2015;Matsuda et al 2015;Pers et al 2015). Association mapping-also known as linkage disequilibrium (LD) mapping-is a promising genetic method for the dissection of complex traits in plants (Ersoz et al 2007;Saidou et al 2014).…”

Nitrogen use efficiency in rapeseed. A review

“…To our knowledge, however, no study so far has elucidated the detailed genetic control of root growth and nutrient responses in B. napus. New methods for automated phenotyping of root responses under controlled conditions (Hatzig et al 2015), in combination with high-resolution genome-wide association studies (Voss-Fels and Snowdon 2015), may help in identifying interesting variants for breeding.…”

Research Article Genetic effects of in vitro germination and plantlet development in chilli pepper.

“…According to Hatzig et al (2015), seed germination was influenced by genetic and environmental factors. In pepper, for example, the germination is affected for temperature stresses (Guo et al, 2012).…”