Genetic dissection of seed characteristics in field pennycress via genome‐wide association mapping studies. Issue 2 (29th April 2022)

• Record Type: Journal Article
• Authors: Tandukar, Zenith; Chopra, Ratan; Frels, Katherine; Heim, Brett; Marks, M. David; Anderson, James A.
• Is Part Of: œplant genome. Volume 15:Issue 2(2022)
• Page Start: n/a
• Page End: n/a
• Publication Date: 2022-04-29
• Subjects: Plant genomes -- Periodicals; Plant genome mapping -- Periodicals; 572.862
• DOI: 10.1002/tpg2.20211
• Languages: English
• ISSNs: 1940-3372

Abstract

Abstract: Field pennycress ( Thlaspi arvense L.) is a new winter annual cash cover crop with high oil content and seed yield, excellent winter hardiness, early maturation, and resistance to most pests and diseases. It provides living cover on fallow croplands between summer seasons, and in doing so reduces nutrient leaching into water sources, mitigates soil erosion, and suppresses weed growth. The first ever genome‐wide association study (GWAS) was conducted on a pennycress diversity panel to identify marker trait associations with important seed size and composition related traits. The entire population was phenotyped in three total environments over 2 yr, and seed area, length, width, thousand grain weight, total oil, and total protein were measured post‐harvest with specialized high‐throughput imaging and near‐infrared spectroscopy. Basic unbiased linear prediction values were calculated for each trait. Seed size traits tended to have higher entry mean reliabilities (0.76–0.79) compared with oil content (0.51) and protein content (0.37). Genotyping‐by‐sequencing identified 33, 606 high quality genome‐wide single nucleotide polymorphism (SNPs) that were coupled with phenotypic data to perform GWAS for seed area, length, width, thousand grain weight, total oil, and total protein content. Fifty‐nine total marker–trait associations were identified revealing genomic regions controlling each trait. The significant SNPs explained 0.06–0.18% of the total variance for that trait in our population. A list of candidate genes was identified based on their functional annotations and characterization in other species. Our results confirm that GWAS is an efficient strategy to identify significant marker–trait associations that can be incorporated into marker‐assisted selection pipelines to accelerate pennycress breeding progress. Core Ideas: Field pennycress is an excellent winter annual oilseed that can serve as a cash cover crop. Genotyping‐by‐sequencing is an effective strategy to genotype pennycress affordably for high‐quality genome‐wide single nucleotide polymorphisms. First‐ever mapping study in a field pennycress association mapping population was conducted. GWAS identified 59 significant marker–trait associations for important quantitative traits. Seed size traits had a higher reliability estimate compared with seed composition traits.