{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,7]],"date-time":"2026-09-07T06:08:18Z","timestamp":1788761298384,"version":"build-2803163510"},"reference-count":37,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,9,7]],"date-time":"2026-09-07T00:00:00Z","timestamp":1788739200000},"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                    Gene banks are essential for conserving plant genetic resources, yet limited genomic characterization constrains their effective use in breeding.\n                    <jats:italic>Coffea arabica<\/jats:italic>\n                    L., an economically important crop in Saudi Arabia, remains poorly characterized at the genome-wide level. We performed whole-genome resequencing of 78 Saudi\n                    <jats:italic>C. arabica<\/jats:italic>\n                    accessions conserved at the Ministry of Environment, Water and Agriculture (MEWA) Seed Center and PGR Bank, generating 86 sequencing libraries, including eight technical replicates. Reads were aligned to the Cara_r6 reference genome, yielding 468, 133 variants (412, 043 SNPs and 56, 090 indels), from which 17, 452 linkage disequilibrium-pruned SNPs were retained for downstream analyses. We identified a pervasive cross-mapping artefact between the homoeologous subgenomes of this allotetraploid species, affecting 63.7% of markers and artificially inflating observed heterozygosity. Correcting this artefact reversed the inbreeding coefficient from negative (FIS \u2248 \u22120.60) to positive (FIS\u00a0=\u00a00.37\u20130.52), consistent with the predominantly self-pollinating biology of\n                    <jats:italic>C. arabica<\/jats:italic>\n                    . Population structure analysis identified seven ancestry groups (K\u00a0=\u00a07) that were highly robust to artefact correction (Adjusted Rand Index = 0.93) but showed no correspondence with collection regions. Analysis of molecular variance attributed only 0.94% of the total genetic variation to differences among regions (p = 0.206). We developed a candidate 150-SNP fingerprinting panel with high marker informativeness (mean PIC\u00a0=\u00a00.374); however, independent validation is required before routine application because closely related accessions could not always be distinguished. These findings provide a robust genomic framework for the conservation and management of Saudi coffee genetic resources and demonstrate the importance of subgenome-aware analytical approaches for whole-genome studies of allotetraploid\n                    <jats:italic>C. arabica<\/jats:italic>\n                    .\n                  <\/jats:p>","DOI":"10.3389\/fpls.2026.1942202","type":"journal-article","created":{"date-parts":[[2026,9,7]],"date-time":"2026-09-07T05:33:54Z","timestamp":1788759234000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Genetic diversity and population structure of Coffea arabica in Saudi Arabia revealed by whole-genome resequencing"],"prefix":"10.3389","volume":"17","author":[{"given":"Naser B.","family":"Almarri","sequence":"first","affiliation":[{"name":"Seed Center and Plant Genetic Resources Bank, Ministry of Environment, Water and Agriculture (MEWA)","place":["Riyadh, Saudi Arabia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sara","family":"Osman","sequence":"additional","affiliation":[{"name":"Seed Center and Plant Genetic Resources Bank, Ministry of Environment, Water and Agriculture (MEWA)","place":["Riyadh, Saudi Arabia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohamed","family":"M. S. Abo El-Enien","sequence":"additional","affiliation":[{"name":"Seed Center and Plant Genetic Resources Bank, Ministry of Environment, Water and Agriculture (MEWA)","place":["Riyadh, Saudi Arabia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Omar A.","family":"Al-Haidar","sequence":"additional","affiliation":[{"name":"Seed Center and Plant Genetic Resources Bank, Ministry of Environment, Water and Agriculture (MEWA)","place":["Riyadh, Saudi Arabia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohanad A.","family":"Ibrahim","sequence":"additional","affiliation":[{"name":"Seed Center and Plant Genetic Resources Bank, Ministry of Environment, Water and Agriculture (MEWA)","place":["Riyadh, Saudi Arabia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Salwa M.","family":"Mostafa","sequence":"additional","affiliation":[{"name":"Seed Center and Plant Genetic Resources Bank, Ministry of Environment, Water and Agriculture (MEWA)","place":["Riyadh, Saudi Arabia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sara M.","family":"Alomran","sequence":"additional","affiliation":[{"name":"Seed Center and Plant Genetic Resources Bank, Ministry of Environment, Water and Agriculture (MEWA)","place":["Riyadh, Saudi Arabia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shakeel","family":"Ahmad","sequence":"additional","affiliation":[{"name":"Seed Center and Plant Genetic Resources Bank, Ministry of Environment, Water and Agriculture (MEWA)","place":["Riyadh, Saudi Arabia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rida","family":"Tariq","sequence":"additional","affiliation":[{"name":"Seed Center and Plant Genetic Resources Bank, Ministry of Environment, Water and Agriculture (MEWA)","place":["Riyadh, Saudi Arabia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rashed","family":"Almarri","sequence":"additional","affiliation":[{"name":"Food and Agriculture Organization of the United Nations (FAO)","place":["Riyadh, Saudi Arabia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ibrahim","family":"Alrashidi","sequence":"additional","affiliation":[{"name":"Seed Center and Plant Genetic Resources Bank, Ministry of Environment, Water and Agriculture (MEWA)","place":["Riyadh, Saudi Arabia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nada M.","family":"Alsofuani","sequence":"additional","affiliation":[{"name":"Seed Center and Plant Genetic Resources Bank, Ministry of Environment, Water and Agriculture (MEWA)","place":["Riyadh, Saudi Arabia"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,9,7]]},"reference":[{"key":"B2","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2020.612593","article-title":"Effectiveness of single nucleotide polymorphism markers in genotyping germplasm collections of Coffea canephora using KASP assay","volume":"11","author":"Akpertey","year":"2021","journal-title":"Front. 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