{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,14]],"date-time":"2026-09-14T06:04:23Z","timestamp":1789365863186,"version":"build-2803163510"},"reference-count":73,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,9,14]],"date-time":"2026-09-14T00:00:00Z","timestamp":1789344000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Plant Sci."],"abstract":"<jats:p>\n                    Rice (\n                    <jats:italic>Oryza sativa<\/jats:italic>\n                    L.) is one of the most important staple crops worldwide, and improving grain yield remains a major objective of rice breeding programs. Yield is a complex quantitative trait influenced by multiple agronomic characteristics, including grain yield per plant (GY), seed setting rate (SSR), plant height (PH), and thousand grain weight (TGW). In this study, a natural population comprising 265 rice accessions was evaluated during two consecutive growing seasons (2022-2023) at one field location, and genome-wide association studies (GWAS) conducted using 4454137 high-quality single nucleotide polymorphisms (SNPs). Best linear unbiased prediction (BLUP) values estimated across the two year-environments were used for association analysis using a mixed linear model (MLM). A total of 102 significant SNPs were identified and consolidated into 20 quantitative trait loci (QTLs), including five associated with GY, four with SSR, ten with PH, and one with TGW. Among them, several loci were co-localized with previously reported genes associated with yield related traits, thereby supporting the reliability of the GWAS results. Candidate gene identification and haplotype analysis further revealed four prioritized genes:\n                    <jats:italic>LOC_Os09g28230 (GID1L2)<\/jats:italic>\n                    for GY,\n                    <jats:italic>LOC_Os05g09500<\/jats:italic>\n                    for SSR,\n                    <jats:italic>LOC_Os03g06930<\/jats:italic>\n                    for PH, and\n                    <jats:italic>LOC_Os02g09170<\/jats:italic>\n                    for TGW. Significant phenotypic differences among haplotypes supported the potential involvement of these genes in regulating the natural trait variation. These findings provide insights into the genetic basis of rice yield related traits and offer genetic resources for future validation and breeding. However, because the present study included only two year-environments at one field location, additional multi-environment validation is required before the broader environmental reproducibility or breeding adaptation.\n                  <\/jats:p>","DOI":"10.3389\/fpls.2026.1909754","type":"journal-article","created":{"date-parts":[[2026,9,14]],"date-time":"2026-09-14T05:39:36Z","timestamp":1789364376000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Genome wide association mapping and haplotype analysis identify genetic loci and candidate genes associated with yield related traits in rice (Oryza sativa L.)"],"prefix":"10.3389","volume":"17","author":[{"given":"Nansheng","family":"Wang","sequence":"first","affiliation":[{"name":"Rice Research Institute, Anhui Academy of Agricultural Sciences","place":["Hefei, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muhammad Ahmad","family":"Hassan","sequence":"additional","affiliation":[{"name":"Rice Research Institute, Anhui Academy of Agricultural Sciences","place":["Hefei, China"]},{"name":"College of Resource and Environment, Anhui Agricultural University","place":["Hefei, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kang","family":"Li","sequence":"additional","affiliation":[{"name":"Rice Research Institute, Anhui Academy of Agricultural Sciences","place":["Hefei, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kunneng","family":"Zhou","sequence":"additional","affiliation":[{"name":"Rice Research Institute, Anhui Academy of Agricultural Sciences","place":["Hefei, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Quan","family":"Gan","sequence":"additional","affiliation":[{"name":"Rice Research Institute, Anhui Academy of Agricultural Sciences","place":["Hefei, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiafa","family":"Xia","sequence":"additional","affiliation":[{"name":"Rice Research Institute, Anhui Academy of Agricultural Sciences","place":["Hefei, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cuixiang","family":"Lin","sequence":"additional","affiliation":[{"name":"Rice Research Institute, Anhui Academy of Agricultural Sciences","place":["Hefei, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zefu","family":"Li","sequence":"additional","affiliation":[{"name":"Rice Research Institute, Anhui Academy of Agricultural Sciences","place":["Hefei, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fengshun","family":"Song","sequence":"additional","affiliation":[{"name":"Rice Research Institute, Anhui Academy of Agricultural Sciences","place":["Hefei, China"]},{"name":"Key Laboratory of Rice Genetics and Breeding in Anhui Province","place":["Hefei, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dahu","family":"Ni","sequence":"additional","affiliation":[{"name":"Rice Research Institute, Anhui Academy of Agricultural Sciences","place":["Hefei, China"]},{"name":"Key Laboratory of Rice Genetics and Breeding in Anhui Province","place":["Hefei, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,9,14]]},"reference":[{"key":"B1","article-title":"Fitting linear mixed-effects models using lme4","volume-title":"Arxiv","author":"Bates","year":"2014"},{"key":"B2","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-642-00296-0_5","article-title":"Pearson correlation coefficient","volume-title":"Noise Reduction in Speech Processing","author":"Benesty","year":"2009"},{"key":"B3","doi-asserted-by":"publisher","first-page":"2633","DOI":"10.1093\/bioinformatics\/btm308","article-title":"TASSEL: Software for association mapping of complex traits in diverse samples","volume":"23","author":"Bradbury","year":"2007","journal-title":"Bioinformatics"},{"key":"B4","doi-asserted-by":"publisher","first-page":"395","DOI":"10.1186\/s12870-019-2007-4","article-title":"NAL8 encodes a prohibitin that contributes to leaf and spikelet development by regulating mitochondria and chloroplasts stability in rice","volume":"19","author":"Chen","year":"2019","journal-title":"BMC Plant Biol."},{"key":"B5","doi-asserted-by":"publisher","first-page":"48","DOI":"10.1186\/s12284-016-0121-6","article-title":"High-resolution QTL mapping for grain appearance traits and co-localization of chalkiness-associated differentially expressed candidate genes in rice","volume":"9","author":"Chen","year":"2016","journal-title":"Rice"},{"key":"B6","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1007\/s11427-021-2024-0","article-title":"Rice functional genomics: Decades\u2019 efforts and roads ahead","volume":"65","author":"Chen","year":"2022","journal-title":"Sci. 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