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ORIGINAL RESEARCH article

Front. Hortic.
Sec. Breeding and Genetics
Volume 3 - 2024 | doi: 10.3389/fhort.2024.1448159

Marker-trait association analysis for easy fruit destemming and mechanical harvestability traits in New Mexican chile pepper (Capsicum annuum L.)

Provisionally accepted
Ehtisham Khokhar Ehtisham Khokhar 1*Dennis Nicuh Lozada Dennis Nicuh Lozada 1,2*Mohsin Ali Mohsin Ali 3Muhammad Ibrar Khan Muhammad Ibrar Khan 1Seyed Shahabeddin Nourbakhsh Seyed Shahabeddin Nourbakhsh 1Stephanie Walker Stephanie Walker 1,2
  • 1 New Mexico State University, Las Cruces, New Mexico, United States
  • 2 Chile Pepper Instiute, Las Cruces, New Mexico, United States
  • 3 Chinese Academy of Agricultural Sciences (CAAS), Beijing, Beijing Municipality, China

The final, formatted version of the article will be published soon.

    Chile pepper (Capsicum annuum L.) mechanization is a promising alternative to traditional hand harvesting due to the costs associated with manual harvest , as well as the increasing unavailability of skilled manual chile harvesters. This study aimed to identify single nucleotide polymorphisms (SNPs) associated with mechanical harvestability (MH) and yield-related traits using multi-locus genome-wide association mapping approaches in a C. annuum association mapping population.Six multi-locus GWAS models identified 12 major SNP markers (R 2 > 10) across nine chromosomes associated with plant architecture, easy destemming traits, and yield parameters.The presence of a major QTL in chromosome P2, dstem2.1, identified recently to be associated with destemming force, was confirmed. Mature green and mature red yield shared three SNP markers mapped on chromosome P3, P5, and P6 explaining 11.94% to 25.15% of the phenotypic variation. Candidate gene analysis for the significant loci identified 19 candidate genes regulating different phytohormone biosynthesis/signaling, metabolic processes, transcription, methylation, DNA repair/replication, and RNA splicing, with potential roles in controlling plant architecture and morphology. The diverse positions of the associated SNPs suggest the complex nature of these quantitative traits, involvement of multiple genetic factors, and novel significant marker-trait associations. Results from this study will be relevant for genetic improvement of mechanical harvestability traits in New Mexican chile pepper using molecular marker-assisted breeding and selection.

    Keywords: Chile pepper mechanization, Genome-Wide Association Study, Genotyping-bysequencing, Quantitative Trait Loci, Single nucleotide polymorphisms

    Received: 12 Jun 2024; Accepted: 30 Jul 2024.

    Copyright: © 2024 Khokhar, Lozada, Ali, Khan, Nourbakhsh and Walker. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence:
    Ehtisham Khokhar, New Mexico State University, Las Cruces, 88003, New Mexico, United States
    Dennis Nicuh Lozada, New Mexico State University, Las Cruces, 88003, New Mexico, United States

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