Association mapping integrated with image-based phenomics identifies SNPs and candidate genes underpinning fruit morphology and development in chile pepper (Capsicum annum L.).

Λεπτομέρειες βιβλιογραφικής εγγραφής
Τίτλος:	Association mapping integrated with image-based phenomics identifies SNPs and candidate genes underpinning fruit morphology and development in chile pepper (Capsicum annum L.).
Συγγραφείς:	Khokhar ES; Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM 88003, United States., Lozada DN; Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM 88003, United States.; Chile Pepper Institute, New Mexico State University, Las Cruces, NM 88003, United States.
Πηγή:	G3 (Bethesda, Md.) [G3 (Bethesda)] 2026 Jul 06; Vol. 16 (7).
Τύπος έκδοσης:	Journal Article; Research Support, U.S. Gov't, Non-P.H.S.
Γλώσσα:	English
Στοιχεία περιοδικού:	Publisher: Oxford University Press Country of Publication: England NLM ID: 101566598 Publication Model: Print Cited Medium: Internet ISSN: 2160-1836 (Electronic) Linking ISSN: 21601836 NLM ISO Abbreviation: G3 (Bethesda) Subsets: MEDLINE
Imprint Name(s):	Publication: 2021- : [Oxford] : Oxford University Press Original Publication: Bethesda, MD : Genetics Society of America, 2011-
Ιατρικοί όροι (MeSH):	Fruit/genetics , Fruit/anatomy & histology , Fruit/growth & development , Capsicum/genetics , Capsicum/growth & development , Capsicum/anatomy & histology , Phenomics/methods , Polymorphism, Single Nucleotide , Chromosome Mapping* , Genetic Association Studies* , Genes, Plant*, Genome-Wide Association Study ; Phenotype ; Quantitative Trait Loci ; Genotype ; Chile
Περίληψη:	Fruit morphology has a significant impact on the agronomic performance of chile peppers, influencing both yield potential and mechanical harvest efficiency. Through the integration of genome-wide association studies (GWAS) with Tomato Analyzer, an image-based phenomics tool, we aim to identify single nucleotide polymorphism (SNP) markers associated with fruit architecture and morphology. A Capsicum association mapping panel (CAMP) consisting of 129 genotypes was evaluated under an augmented field design for the 2024 growing season in New Mexico, United States. Best linear unbiased predictions (BLUPs) were reported for maximum fruit height (MAXH), maximum fruit width (MAXW), curved fruit height (CURH), width mid-height (WMH), height mid-width (HMW), area (ARA), perimeter (PER), 10-pod weight (PODW), and yield (YLD). Medium to low narrow-sense heritability (h2), ranging between 0.18 and 0.33, was observed. A medium to high Pearson correlation (r = 0.23 to 1.00) was observed for all traits except WMH. After filtration and imputation, 40,709 genotyping-by-sequencing (GBS) SNP markers were used to perform multilocus GWAS. A total of 169 SNP markers associated with seven basic fruit measurements across 12 chromosomes were identified. A SNP marker, SCM002812.1_10016804 on chromosome 1, identified across multiple GWAS models was found to be associated with the potential candidate gene, YABBY4, which can regulate fruit development. Other candidate genes identified included FRIGIDA-like protein 3, COBRA-like protein, and auxin-responsive protein SAUR65 regulating flower, fruit, and shoot development. The findings of this study will be relevant for the development of molecular markers for marker-assisted selection, genomic selection for basic fruit morphology traits, and studying expression levels of genes regulating fruit development in chile peppers. (© The Author(s) 2026. Published by Oxford University Press on behalf of The Genetics Society of America.)
References:	PLoS One. 2020 Aug 17;15(8):e0237741. (PMID: 32804977) Heredity (Edinb). 2017 Jun;118(6):517-524. (PMID: 28295030) Int J Mol Sci. 2024 Nov 04;25(21):. (PMID: 39519386) Bioinformatics. 2014 Aug 1;30(15):2114-20. (PMID: 24695404) Phytopathology. 2023 Jun;113(6):921-930. (PMID: 36401843) Ann Bot. 2016 Jul;118(1):35-51. (PMID: 27245634) Int J Mol Sci. 2019 Nov 13;20(22):. (PMID: 31766117) Front Plant Sci. 2020 Jul 23;11:1100. (PMID: 32793261) Int J Mol Sci. 2022 Sep 10;23(18):. (PMID: 36142418) BMC Plant Biol. 2012 Nov 10;12:211. (PMID: 23140186) Heredity (Edinb). 2018 Mar;120(3):208-218. (PMID: 29234158) Front Plant Sci. 2019 Jul 09;10:886. (PMID: 31354762) Plant J. 2009 Mar;57(5):918-31. (PMID: 19121105) G3 (Bethesda). 2015 Sep 15;5(11):2383-90. (PMID: 26377960) Plant Genome. 2018 Mar;11(1):. (PMID: 29505638) Methods Mol Biol. 2016;1374:115-40. (PMID: 26519403) Mol Ecol. 2005 Jul;14(8):2611-20. (PMID: 15969739) Bioinformatics. 2010 Mar 1;26(5):589-95. (PMID: 20080505) PLoS Comput Biol. 2017 Jan 31;13(1):e1005357. (PMID: 28141824) Sci Rep. 2016 Jan 20;6:19444. (PMID: 26787347) Bioinformatics. 2007 Oct 1;23(19):2633-5. (PMID: 17586829) PLoS One. 2016 Jun 06;11(6):e0156744. (PMID: 27271781) Plant Genome. 2021 Mar;14(1):e20077. (PMID: 33442955) Plant Mol Biol. 2005 Mar;57(4):461-85. (PMID: 15821975) Front Plant Sci. 2019 Oct 08;10:1207. (PMID: 31649691) Plant J. 2023 Dec;116(5):1508-1528. (PMID: 37602679) Sci Rep. 2019 Jun 11;9(1):8446. (PMID: 31186437) Theor Appl Genet. 2003 May;106(8):1457-66. (PMID: 12750789) Mol Plant. 2020 Feb 3;13(2):187-214. (PMID: 31981735) Mol Ecol Resour. 2017 Jan;17(1):27-32. (PMID: 26850166) Front Plant Sci. 2019 Feb 11;10:100. (PMID: 30804969) Sci Rep. 2019 Jul 11;9(1):10067. (PMID: 31296904) J Vis Exp. 2010 Mar 16;(37):. (PMID: 20234339) Genome. 2013 Jan;56(1):61-74. (PMID: 23379339) DNA Res. 2016 Apr;23(2):81-91. (PMID: 26744365) BMC Genomics. 2021 May 17;22(1):356. (PMID: 34000992) BMC Plant Biol. 2024 May 17;24(1):416. (PMID: 38760676) Bioinformatics. 2012 Jan 15;28(2):298-9. (PMID: 22110245) Brief Bioinform. 2018 Jul 20;19(4):700-712. (PMID: 28158525) Plants (Basel). 2023 May 22;12(10):. (PMID: 37653978) Proc Natl Acad Sci U S A. 2014 Apr 8;111(14):5135-40. (PMID: 24591624) Plant Cell. 2022 Feb 3;34(2):818-833. (PMID: 34850922) Plant Cell Physiol. 2001 May;42(5):524-30. (PMID: 11382819) Nat Genet. 2008 Jun;40(6):800-4. (PMID: 18469814) Genomics Proteomics Bioinformatics. 2020 Aug;18(4):481-487. (PMID: 33346083) Genetics. 2000 Jun;155(2):945-59. (PMID: 10835412) Front Plant Sci. 2022 May 03;13:879182. (PMID: 35592583) Plant Genome. 2017 Nov;10(3):. (PMID: 29293816) Front Genet. 2023 May 15;14:1101401. (PMID: 37255716) Sci Rep. 2016 Nov 30;6:38081. (PMID: 27901114) BMC Genomics. 2019 Jun 11;20(1):481. (PMID: 31185892) PLoS One. 2019 May 21;14(5):e0216886. (PMID: 31112575) Nat Rev Genet. 2019 Aug;20(8):467-484. (PMID: 31068683) Sci Rep. 2025 Apr 9;15(1):12161. (PMID: 40204786) Int J Plant Genomics. 2008;2008:574927. (PMID: 18551188)
Grant Information:	2022-67014-37078 USDA NIFA; New Mexico Chile Association
Contributed Indexing:	Keywords: fruit phenotypic diversity; image-based phenomics platform; marker–trait association analysis
Entry Date(s):	Date Created: 20260502 Date Completed: 20260706 Latest Revision: 20260813
Update Code:	20260813
PubMed Central ID:	PMC13334168
DOI:	10.1093/g3journal/jkag116
PMID:	42068164
Βάση Δεδομένων:	MEDLINE

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ISSN:	2160-1836
DOI:	10.1093/g3journal/jkag116