Chile Pepper (Capsicum) Breeding and Improvement in the "Multi-Omics" Era

Dennis N Lozada; Paul W Bosland; Derek W Barchenger; Mahdi Haghshenas-Jaryani; Soumaila Sanogo; Stephanie Walker

doi:10.3389/fpls.2022.879182

Chile Pepper (Capsicum) Breeding and Improvement in the "Multi-Omics" Era

Front Plant Sci. 2022 May 3:13:879182. doi: 10.3389/fpls.2022.879182. eCollection 2022.

Authors

Dennis N Lozada^{1

2}, Paul W Bosland^{1

2}, Derek W Barchenger³, Mahdi Haghshenas-Jaryani⁴, Soumaila Sanogo⁵, Stephanie Walker^{2

6}

Affiliations

¹ Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, United States.
² Chile Pepper Institute, New Mexico State University, Las Cruces, NM, United States.
³ World Vegetable Center, Tainan, Taiwan.
⁴ Department of Mechanical and Aerospace Engineering, New Mexico State University, Las Cruces, NM, United States.
⁵ Department of Entomology, Plant Pathology and Weed Science, New Mexico State University, Las Cruces, NM, United States.
⁶ Department of Extension Plant Sciences, New Mexico State University, Las Cruces, NM, United States.

Abstract

Chile pepper (Capsicum spp.) is a major culinary, medicinal, and economic crop in most areas of the world. For more than hundreds of years, chile peppers have "defined" the state of New Mexico, USA. The official state question, "Red or Green?" refers to the preference for either red or the green stage of chile pepper, respectively, reflects the value of these important commodities. The presence of major diseases, low yields, decreased acreages, and costs associated with manual labor limit production in all growing regions of the world. The New Mexico State University (NMSU) Chile Pepper Breeding Program continues to serve as a key player in the development of improved chile pepper varieties for growers and in discoveries that assist plant breeders worldwide. Among the traits of interest for genetic improvement include yield, disease resistance, flavor, and mechanical harvestability. While progress has been made, the use of conventional breeding approaches has yet to fully address producer and consumer demand for these traits in available cultivars. Recent developments in "multi-omics," that is, the simultaneous application of multiple omics approaches to study biological systems, have allowed the genetic dissection of important phenotypes. Given the current needs and production constraints, and the availability of multi-omics tools, it would be relevant to examine the application of these approaches in chile pepper breeding and improvement. In this review, we summarize the major developments in chile pepper breeding and present novel tools that can be implemented to facilitate genetic improvement. In the future, chile pepper improvement is anticipated to be more data and multi-omics driven as more advanced genetics, breeding, and phenotyping tools are developed.

Keywords: Phytophthora capsici resistance; genome-wide association study; genomic selection; heat profile; high-throughput phenotyping; single nucleotide polymorphisms; speed breeding; yield.

Publication types

Review