Genetic analysis and QTL mapping of domestication-related traits in chili pepper (Capsicum annuum L.)

Authors: LOPEZ-MORENO, HECTOR - University Of Wisconsin; BASURTO-GARDUNO, ANA - Langebio Cinvestav; TORRES-MERAZ, MARIA - University Of Wisconsin; DIAZ-VALENZUELA, ERIC - Langebio Cinvestav; ARELLANO-ARCINIEGA, SERGIO - Instituto Nacional De Investigaciones Forestales Y Agropecuarias (INIFAP); Zalapa, Juan; SAWERS, RUAIRIDH - Pennsylvania State University; CIBRIAN-JARAMILLO, ANGELICA - Langebio Cinvestav; DIAZ-GARCIA, LUIS - University Of California, Davis

Submitted to: Frontiers in Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/31/2023
Publication Date: 5/15/2023
Citation: Lopez-Moreno, H., Basurto-Garduno, A.C., Torres-Meraz, M.A., Diaz-Valenzuela, E., Arellano-Arciniega, S., Zalapa, J.E., Sawers, R.J., Cibrian-Jaramillo, A., Diaz-Garcia, L. 2023. Genetic analysis and QTL mapping of domestication-related traits in chili pepper (Capsicum annuum L.). Frontiers in Genetics. 14: 1-14. https://doi.org/10.3389/fgene.2023.1101401.
DOI: https://doi.org/10.3389/fgene.2023.1101401

Interpretive Summary: Chili pepper (Capsicum annuum L.) is one of the oldest and most phenotypically diverse pre-Columbian crops of the Americas. Despite the abundance of genetic resources, the use of wild germplasm and landraces in chili pepper breeding is limited. A better understanding of the evolutionary history in chili peppers, particularly in the context of traits of agronomic interest, can contribute to future improvement and conservation of genetic resources. In this study, an F2:F3 mapping population derived from a cross between a C. annuum wild accession (Chiltepin) and a cultivated variety (Puya) was used to identify genomic regions associated with 19 domestication and agronomic traits. A genetic map was constructed consisting of 1023 single nucleotide polymorphism (SNP) markers clustered into 12 linkage groups and spanning a total of 1263.87 cM. A reciprocal translocation that differentiates the domesticated genome from its wild ancestor and other related species was identified between chromosomes 1 and 8. Quantitative trait locus (QTL) analysis detected 20 marker-trait associations for 13 phenotypes, from which 14 corresponded to previously identified loci, and six were novel genomic regions related to previously unexplored domestication-syndrome traits, including form of unripe fruit, seedlessness, deciduous fruit, and growth habit. Our results revealed that the genetic architecture of Capsicum domestication is similar to other domesticated species with few loci with large effects, the presence of QTLs clusters in different genomic regions, and the predominance of domesticated recessive alleles. Our analysis indicates the domestication process in chili pepper has also had an effect on traits not directly related to the domestication syndrome. The information obtained in this study provides a more complete understanding of the genetic basis of Capsicum domestication that can potentially guide strategies for the exploitation of wild alleles.

Technical Abstract: Chili pepper (Capsicum annuum L.) is one of the oldest and most phenotypically diverse pre-Columbian crops of the Americas. Despite the abundance of genetic resources, the use of wild germplasm and landraces in chili pepper breeding is limited. A better understanding of the evolutionary history in chili peppers, particularly in the context of traits of agronomic interest, can contribute to future improvement and conservation of genetic resources. In this study, we used a chili pepper population derived from a cross between a wild chili called Chiltepin and a cultivated variety (Puya) to identify genes controlling 19 domestication and agronomic traits. A genetic map was constructed for the cross and 20 marker-trait associations were detected for 13 phenotypes, from which 14 corresponded to previously identified genes, and six were novel genes related to previously unexplored domestication-syndrome traits, including form of unripe fruit, seedlessness, deciduous fruit, and growth habit. Our results revealed that the genetic architecture of chili pepper domestication is similar to other domesticated species with few genes with large effects, the presence of gens clusters in different chromosome regions, and the predominance of domesticated recessive gene variants. Our analysis indicates the domestication process in chili pepper has also had an effect on traits not directly related to the domestication syndrome. The information obtained in this study provides a more complete understanding of the genetic basis of chili pepper domestication that can potentially guide strategies for the exploitation of wild chili peppers.