Genome-wide analyses reveal footprints of divergent selection and popping-related traits in CIMMYT’s maize inbred lines
Popcorn (Zea mays L. var. Everta) is the most ancient type of cultivated maize. However, there is little known about the genetics of popping-related traits based on genotyping-by-sequencing (GBS) technology. Here, we characterized the phenotypic variation for seven popping-related traits in maize ke...
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| Format: | article |
| Language: | English |
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2020
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| Online Access: | https://hdl.handle.net/20.500.12381/3971 https://doi.org/10.1093/jxb/eraa480 |
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| _version_ | 1868890099472662528 |
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| author | Li, Jing |
| author2 | Li, Delin Zavala Espinosa, Cristian Trejo Pastor, Viridiana Rasheed, Awais Palacios Rojas, Natalia Wang, Jiankang Santacruz Varela, Amalio de Almeida Silva, Natália Carolina Schnable, Patrick Costich, Denise Li, Huihui |
| author2_role | author author author author author author author author author author author |
| author_browse | Costich, Denise Li, Delin Li, Huihui Li, Jing Palacios Rojas, Natalia Rasheed, Awais Santacruz Varela, Amalio Schnable, Patrick Trejo Pastor, Viridiana Wang, Jiankang Zavala Espinosa, Cristian de Almeida Silva, Natália Carolina |
| author_facet | Li, Jing Li, Delin Zavala Espinosa, Cristian Trejo Pastor, Viridiana Rasheed, Awais Palacios Rojas, Natalia Wang, Jiankang Santacruz Varela, Amalio de Almeida Silva, Natália Carolina Schnable, Patrick Costich, Denise Li, Huihui |
| author_role | author |
| collection | UTEC en REDI |
| dc.creator.none.fl_str_mv | Li, Jing Li, Delin Zavala Espinosa, Cristian Trejo Pastor, Viridiana Rasheed, Awais Palacios Rojas, Natalia Wang, Jiankang Santacruz Varela, Amalio de Almeida Silva, Natália Carolina Schnable, Patrick Costich, Denise Li, Huihui |
| dc.date.none.fl_str_mv | 2020 2025-05-09T13:28:25Z 2025-05-09T13:28:25Z |
| dc.identifier.none.fl_str_mv | https://hdl.handle.net/20.500.12381/3971 https://doi.org/10.1093/jxb/eraa480 |
| dc.language.none.fl_str_mv | eng |
| dc.publisher.none.fl_str_mv | Oxford University Press Society for Experimental Biology (SEB) |
| dc.rights.none.fl_str_mv | Acceso abierto info:eu-repo/semantics/openAccess Reconocimiento 4.0 Internacional. (CC BY) |
| dc.source.none.fl_str_mv | Journal of Experimental Botany, Volume 72 reponame:UTEC en REDI instname:Universidad Tecnológica instacron:Universidad Tecnológica |
| dc.subject.none.fl_str_mv | EigenGWAS GWAS Maize adaptation Popping traits Quality traits Tropical maize landrace Ciencias Naturales y Exactas Ciencias Biológicas Genética y Herencia |
| dc.title.none.fl_str_mv | Genome-wide analyses reveal footprints of divergent selection and popping-related traits in CIMMYT’s maize inbred lines |
| dc.type.none.fl_str_mv | Artículo info:eu-repo/semantics/article Publicado info:eu-repo/semantics/publishedVersion |
| description | Popcorn (Zea mays L. var. Everta) is the most ancient type of cultivated maize. However, there is little known about the genetics of popping-related traits based on genotyping-by-sequencing (GBS) technology. Here, we characterized the phenotypic variation for seven popping-related traits in maize kernels among 526 CIMMYT inbred lines (CMLs). In total, 155 083 high-quality single nucleotide polymorphism (SNP) markers were identified by a GBS approach. Several trait-associated loci were detected by genome-wide association study for color, popping expansion volume, shape, pericarp, flotation index, floury/vitreous, and protein content, explaining a majority of the observed phenotypic variance, and these were validated by a diverse panel comprising 764 tropical landrace accessions. Sixty two of the identified loci were recognized to have undergone selection. On average, there was a 55.27% frequency for alleles that promote popping in CMLs. Our work not only pinpoints previously unknown loci for popping-related traits, but also reveals that many of these loci have undergone selection. Beyond establishing a new benchmark for the genetics of popcorn, our study provides a foundation for gene discovery and breeding. It also presents evidence to investigate the role of a gradual loss of popping ability as a by-product of diversification of culinary uses throughout the evolution of teosinte–to–modern maize. |
| eu_rights_str_mv | openAccess |
| format | article |
| id | anni_77c2337c8e50a0285a7de3ce7e1a1bb0 |
| instacron_str | Universidad Tecnológica |
| institution | Universidad Tecnológica |
| instname_str | Universidad Tecnológica |
| language | eng |
| network_acronym_str | anni |
| network_name_str | oai-lr-anni |
| oai_identifier_str | oai:redi.anii.org.uy:20.500.12381/3971 |
| publishDate | 2020 |
| publishDateSort | 2020 |
| publisher.none.fl_str_mv | Oxford University Press Society for Experimental Biology (SEB) |
| reponame_str | UTEC en REDI |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | Acceso abierto Reconocimiento 4.0 Internacional. (CC BY) |
| spelling | Genome-wide analyses reveal footprints of divergent selection and popping-related traits in CIMMYT’s maize inbred linesLi, JingLi, DelinZavala Espinosa, CristianTrejo Pastor, ViridianaRasheed, AwaisPalacios Rojas, NataliaWang, JiankangSantacruz Varela, Amaliode Almeida Silva, Natália CarolinaSchnable, PatrickCostich, DeniseLi, HuihuiEigenGWASGWASMaize adaptationPopping traitsQuality traitsTropical maize landraceCiencias Naturales y ExactasCiencias BiológicasGenética y HerenciaPopcorn (Zea mays L. var. Everta) is the most ancient type of cultivated maize. However, there is little known about the genetics of popping-related traits based on genotyping-by-sequencing (GBS) technology. Here, we characterized the phenotypic variation for seven popping-related traits in maize kernels among 526 CIMMYT inbred lines (CMLs). In total, 155 083 high-quality single nucleotide polymorphism (SNP) markers were identified by a GBS approach. Several trait-associated loci were detected by genome-wide association study for color, popping expansion volume, shape, pericarp, flotation index, floury/vitreous, and protein content, explaining a majority of the observed phenotypic variance, and these were validated by a diverse panel comprising 764 tropical landrace accessions. Sixty two of the identified loci were recognized to have undergone selection. On average, there was a 55.27% frequency for alleles that promote popping in CMLs. Our work not only pinpoints previously unknown loci for popping-related traits, but also reveals that many of these loci have undergone selection. Beyond establishing a new benchmark for the genetics of popcorn, our study provides a foundation for gene discovery and breeding. It also presents evidence to investigate the role of a gradual loss of popping ability as a by-product of diversification of culinary uses throughout the evolution of teosinte–to–modern maize.Oxford University PressSociety for Experimental Biology (SEB)2025-05-09T13:28:25Z2025-05-09T13:28:25Z2020Artículoinfo:eu-repo/semantics/articlePublicadoinfo:eu-repo/semantics/publishedVersionhttps://hdl.handle.net/20.500.12381/3971https://doi.org/10.1093/jxb/eraa480Journal of Experimental Botany, Volume 72reponame:UTEC en REDIinstname:Universidad Tecnológicainstacron:Universidad TecnológicaengAcceso abiertoinfo:eu-repo/semantics/openAccessReconocimiento 4.0 Internacional. (CC BY)oai:redi.anii.org.uy:20.500.12381/39712026-06-16T05:30:18Z |
| spellingShingle | Genome-wide analyses reveal footprints of divergent selection and popping-related traits in CIMMYT’s maize inbred lines Li, Jing EigenGWAS GWAS Maize adaptation Popping traits Quality traits Tropical maize landrace Ciencias Naturales y Exactas Ciencias Biológicas Genética y Herencia |
| status_str | publishedVersion |
| title | Genome-wide analyses reveal footprints of divergent selection and popping-related traits in CIMMYT’s maize inbred lines |
| title_full | Genome-wide analyses reveal footprints of divergent selection and popping-related traits in CIMMYT’s maize inbred lines |
| title_fullStr | Genome-wide analyses reveal footprints of divergent selection and popping-related traits in CIMMYT’s maize inbred lines |
| title_full_unstemmed | Genome-wide analyses reveal footprints of divergent selection and popping-related traits in CIMMYT’s maize inbred lines |
| title_short | Genome-wide analyses reveal footprints of divergent selection and popping-related traits in CIMMYT’s maize inbred lines |
| title_sort | Genome-wide analyses reveal footprints of divergent selection and popping-related traits in CIMMYT’s maize inbred lines |
| topic | EigenGWAS GWAS Maize adaptation Popping traits Quality traits Tropical maize landrace Ciencias Naturales y Exactas Ciencias Biológicas Genética y Herencia |
| url | https://hdl.handle.net/20.500.12381/3971 https://doi.org/10.1093/jxb/eraa480 |