{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,8,3]],"date-time":"2025-08-03T22:50:37Z","timestamp":1754261437160,"version":"3.37.3"},"reference-count":41,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2021,10,2]],"date-time":"2021-10-02T00:00:00Z","timestamp":1633132800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100014343","name":"National Tea Research Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100014343","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Ministry of Commerce"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Tea is a cross-pollinated woody perennial plant, which is why, application of conventional breeding is limited for its genetic improvement. However, lack of the genome-wide high-density SNP markers and genome-wide haplotype information has greatly hampered the utilization of tea genetic resources toward fast-track tea breeding programs. To address this challenge, we have generated a first-generation haplotype map of tea (Tea HapMap-1). Out-crossing and highly heterozygous nature of tea plants, make them more complicated for DNA-level variant discovery.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>In this study, whole genome re-sequencing data of 369 tea genotypes were used to generate 2,334,564 biallelic SNPs and 1,447,985 InDels. Around 2928.04 million paired-end reads were used with an average mapping depth of \u223c0.31\u00d7 per accession. Identified polymorphic sites in this study will be useful in mapping the genomic regions responsible for important traits of tea. These resources lay the foundation for future research to understand the genetic diversity within tea germplasm and utilize genes that determine tea quality. This will further facilitate the understanding of tea genome evolution and tea metabolite pathways thus, offers an effective germplasm utilization for breeding the tea varieties.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab690","type":"journal-article","created":{"date-parts":[[2021,9,30]],"date-time":"2021-09-30T16:18:42Z","timestamp":1633018722000},"page":"318-324","source":"Crossref","is-referenced-by-count":2,"title":["A first-generation haplotype map (HapMap-1) of tea (<i>Camellia sinensis<\/i> L. O. Kuntz)"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1950-815X","authenticated-orcid":false,"given":"Nisha","family":"Singh","sequence":"first","affiliation":[{"name":"ICAR-National Institute for Plant Biotechnology, LBS Building, Pusa campus , New Delhi 110012, India"}]},{"given":"Hukam C","family":"Rawal","sequence":"additional","affiliation":[{"name":"ICAR-National Institute for Plant Biotechnology, LBS Building, Pusa campus , New Delhi 110012, India"}]},{"given":"Ulavappa B","family":"Angadi","sequence":"additional","affiliation":[{"name":"ICAR-Indian Agricultural Statistics Research Institute , New Delhi 110012, India"}]},{"given":"Tilak Raj","family":"Sharma","sequence":"additional","affiliation":[{"name":"ICAR-National Institute for Plant Biotechnology, LBS Building, Pusa campus , New Delhi 110012, India"}]},{"given":"Nagendra Kumar","family":"Singh","sequence":"additional","affiliation":[{"name":"ICAR-National Institute for Plant Biotechnology, LBS Building, Pusa campus , New Delhi 110012, India"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6702-2990","authenticated-orcid":false,"given":"Tapan Kumar","family":"Mondal","sequence":"additional","affiliation":[{"name":"ICAR-National Institute for Plant Biotechnology, LBS Building, Pusa campus , New Delhi 110012, India"}]}],"member":"286","published-online":{"date-parts":[[2021,10,2]]},"reference":[{"key":"2023020108465195600_btab690-B1","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1186\/1297-9686-46-35","article-title":"Single nucleotide polymorphism and haplotype effects associated with somatic cell score in German Holstein cattle","volume":"46","author":"Abdel-Shafy","year":"2014","journal-title":"Genet Sel Evol"},{"key":"2023020108465195600_btab690-B2","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1038\/nature11632","article-title":"An integrated map of genetic variation from 1,092 human genomes","volume":"491","author":"Abecasis","year":"2012","journal-title":"Nature"},{"key":"2023020108465195600_btab690-B3","doi-asserted-by":"crossref","first-page":"648229","DOI":"10.3389\/fgene.2021.648229","article-title":"A benchmark of genetic variant calling pipelines using metagenomic short-read sequencing","volume":"12","author":"Andreu-S\u00e1nchez","year":"2021","journal-title":"Front. 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