Identification of heat tolerance loci in broccoli through bulked segregant analysis using whole genome resequencing

Authors: Branham, Sandra; Farnham, Mark

Submitted to: Euphytica
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/21/2018
Publication Date: 2/5/2019
Citation: Branham, S., Farnham, M.W. 2019. Identification of heat tolerance loci in broccoli through bulked segregant analysis using whole genome resequencing. Euphytica. 215:34.

Interpretive Summary: Broccoli has emerged in recent decades as one of the most important vegetable crops produced in the United States, now valued at close to 900 million dollars annually. When heat stress occurs during the early stages of broccoli head development, the resulting head will often exhibit undesirable attributes like irregular head shape, leafiness, and uneven bead size, all of which can have a negative impact on quality and marketable yield of the resulting harvested vegetable. In fact, the likelihood that high temperature will occur in a given location or season is the primary factor limiting where and when the crop can be grown. ARS scientists at Charleston, South Carolina have developed broccoli that is better adapted to a hot environment and use of these high temperature-adapted types could extend the growing season of broccoli, expand production areas for the crop, and increase resilience to fluctuating temperatures. However, there is still a lack of genetic knowledge about the heat tolerance trait. Thus, the same ARS scientists in Charleston evaluated two groups of closely related broccoli lines that differ in their response to heat, with one adapted group able to produce high quality heads during a hot South Carolina summer, and a second un-adapted group that produces damaged, unmarketable heads in the same season. The scientists analyzed the DNA sequences of the two groups and were able to identify specific sequences that appear to be associated with the ability to tolerate high temperatures and produce quality broccoli heads. The identified sequences are of great interest to public and private broccoli breeders working to accelerate the development of broccoli cultivars that are better adapted to hot conditions.

Technical Abstract: Most broccoli cultivars are sensitive to high temperatures during the early stages of floral development causing a severe decline of head quality or even complete lack of head formation under superoptimal crop production temperatures. Several heat tolerant lines have been developed in recent years but there have been few studies of the genetic basis of this complex, polygenic trait. A doubled haploid population of broccoli was evaluated for head quality across two summer field trials with the phenotypic extremes validated in two additional summer fields. Whole-genome resequencing of the bulked segregants was used for a QTL-seq analysis of heat tolerance, which identified two novel quantitative trait loci (QTL) different than those previously identified. Nonsynonymous SNPs were found in a block of flowering time genes within QHT_C09.2 and may explain the significant negative correlation between time to head maturity and heat tolerance. Breeding further genetic gains in this complex, polygenic trait could be expedited through marker assisted selection and gene pyramiding using markers developed from the QTL identified herein.