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ARS Home » Plains Area » Fargo, North Dakota » Edward T. Schafer Agricultural Research Center » Weed and Insect Biology Research » Research » Publications at this Location » Publication #406014
Research Project: Biology of Weed-Crop Interactions to Improve Weed Management Strategies in Northern Agro-ecosystems

Location: Weed and Insect Biology Research

Title: Genome-wide association study and genomic prediction for pod shatter resistance in a diverse rapeseed/canola germplasm collection

Author
item HOSAIN, SHAKIL - North Dakota State University
item ROY, JAYANTA - North Dakota State University
item Horvath, David
item ARIFUZZAMAN, MUHAMMAD - University Of Missouri
item HOQUE, AHASANUL - Bangladesh Agricultural University
item MUKHLESUR, RAHMAN - North Dakota State University

Submitted to: Molecular Breeding
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/4/2025
Publication Date: N/A
Citation: N/A

Interpretive Summary: Canola yield is reduced when its seedpods shatter before and during harvest as combines first hit the plants but before the pods are collected. Developing canola varieties that have reduced shattering will greatly increase yield, and thus profits for growers. To assist breeders in developing shatter resistant canola, a team of researchers quantified differences in shattering resistance in a diverse population of canola whose members had been previously sequenced. This allowed the team to identify 21 different regions of the genome and multiple individual genes that were more likely to be associated with shattering resistance. Additionally, the team was able to use this information to predict the level of shattering resistance in previously uncharacterized individuals. This information provides insight into the mechanisms that influence pod shattering in canola, and also provides canola breeders with the tools needed to speed up breeding for shattering resistance.

Technical Abstract: Pod-shattering in rapeseed/canola results in significant yield loss. In this study, a diverged spring-type rapeseed/canola germplasm consisting of 140 accessions was evaluated for pod-shattering resistance in five environments under field and greenhouse conditions. The genome-wide association study (GWAS) was conducted using 24k single nucleotide polymorphisms (SNPs) markers. Eight GWAS methods were employed which identified 21 SNPs for pod-shattering. The phenotypic variation explained by these SNPs ranged from 3.8 -25.4%. The SNPs positions located on chromosomes A03, A09, C03 have been previously reported to be associated with shattering. two strong candidate genes, INDEHISCENT (IND), and MANNANASE7 (MAN7), located on chromosome A03 (20.5 Mbp position), chromosome C03 (53.7 Mbp position), respectively, were identified for the pod shatter trait. Genomic prediction (GP) was conducted with 24k SNPs using 14 prediction models. The prediction ability of all models ranged from 0.18 – 0.50. To determine the minimum number of markers needed to estimate the predictive ability, we used 25 to 20000 randomly selected markers where 3000 to 20000 markers gave a similar prediction ability (˜0.47). This study provides significant insight and elevates our understanding of the genetic architecture of pod-shattering in canola and suggests that GP has the potential to select pod shatter resistance germplasm at an early stage to use in a breeding program.