Discovery of major quantitative trait loci and candidate genes for fresh seed dormancy in groundnut

Authors: BOMIREDDY, DEEKSHITHA - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; GANGURDE, SUNIL - University Of Georgia; VARIATH, MURALI - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; JANILA, PASPUPULETI - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; MANOHAR, SURENDRA - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; SHARMA, VINAY - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; PARMAR, SEJAL - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; DESHMUKH, DNYANESHWAR - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; MANGALA, REDDISEKHAR - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; MOHAN REDDY, DEVARAPALLI - Insitute Of Frontier Technologies-Rars; SUDHAKAR, PALAGIRI - Sv Agricultural College; BHASKARA REDDY, BOMMU VEERA - Insitute Of Frontier Technologies-Rars; VARSHNEY, RAJEEV - Murdoch University; Guo, Baozhu; PANDEY, MANISH - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India

Submitted to: Agronomy
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/3/2022
Publication Date: 2/6/2022
Citation: Bomireddy, D., Gangurde, S.S., Variath, M.T., Janila, P., Manohar, S.S., Sharma, V., Parmar, S., Deshmukh, D., Mangala, R., Mohan Reddy, D., Sudhakar, P., Bhaskara Reddy, B., Varshney, R.K., Guo, B., Pandey, M.K. 2022. Discovery of major quantitative trait loci and candidate genes for fresh seed dormancy in groundnut. Agronomy. 12(2):404. https://doi.org/10.3390/agronomy12020404.
DOI: https://doi.org/10.3390/agronomy12020404

Interpretive Summary: Peanut is a widely grown oilseed crop, that belongs to the family of Leguminosae or Fabaceae. Global production of peanut is 66.3 million tons, covering 34.1 million hectares of cultivated area making it the third-largest oilseed crop. There are certain widespread constraints affecting peanut yield. In-situ germination of freshly matured seeds at the time of harvesting is one such potential constraint limiting the production as well as quality. Generally, Spanish market-genotype is early maturing and lacks fresh seed dormancy (FSD). Therefore, with late season rainfall prior to harvesting, seeds of Spanish genotypes tend to germinate in pods inside the soil, leading to reduced yield and quality. Plant growth regulators such as abscisic acid (ABA) have been known to positively regulate dormancy, whereas gibberellins (GA) and ethylene tend to break the dormancy. In this study, five major QTLs were identified associated with FSD. A total of 25 candidate genes were identified based on differential gene expression analysis. The identified genomic regions and candidate genes can be further used to develop allele-specific markers for potential marker-assisted breeding to improve the seed dormancy trait in peanut.

Technical Abstract: The in-situ germination or pre-harvest sprouting of peanut seeds results in substantial yield reduction and quality. Spanish bunch peanut varieties are cultivated in the most area in Asia and Africa, with the problem of lacking fresh seed dormancy (FSD). Genomic breeding can help to improve commercial peanut cultivars with 2-3 weeks of dormancy. Therefore, a recombinant inbred line (RIL) population derived from the cross between ICGV 02266 (Non-dormant) × ICGV 97045 (Dormant) was used to identify the genomic regions associated with fresh seed dormancy. The RIL population was genotyped with a genotyping assay of 5K SNPs and a linkage map was constructed with 325 SNP loci spanning a map length of 2335.3 cM. The quantitative trait locus (QTL) analysis using two seasons of phenotyping data and the genetic map information identified five major QTLs on chromosomes A01 and B01, A06, and B06, and B07. A total of 25 potential candidate genes were identified from these QTL regions. The differential gene expression was established using transcriptomic information from dormant (Tifrunner) and non-dormant (ICGV 91114) genotypes. We concluded that, histone deacetylases, histone-lysine N-methyltransferase, cytochrome P450, protein kinases, and ethylene-responsive transcription factor are the key regulators involved in hormonal regulation of abscisic acid, gibberellic acid, and ethylene biosynthesis pathways. The identified genes and markers need to be validated for potential use in breeding of new varieties with FSD using marker-assisted selection.