{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,31]],"date-time":"2026-10-31T00:58:19Z","timestamp":1793408299368,"version":"4.5.0"},"reference-count":31,"publisher":"Wiley","issue":"3","license":[{"start":{"date-parts":[[2019,11,1]],"date-time":"2019-11-01T00:00:00Z","timestamp":1572566400000},"content-version":"am","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"},{"start":{"date-parts":[[2019,11,1]],"date-time":"2019-11-01T00:00:00Z","timestamp":1572566400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000199","name":"U.S. Department of Agriculture","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000199","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["acsess.onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["The Plant Genome"],"published-print":{"date-parts":[[2019,11]]},"abstract":"<jats:sec>\n                    <jats:title>Core Ideas<\/jats:title>\n                    <jats:p>\n                      <jats:list list-type=\"bullet\">\n                        <jats:list-item>\n                          <jats:p>Genomic data from diverse germplasm used for application in targeted breeding germplasm.<\/jats:p>\n                        <\/jats:list-item>\n                        <jats:list-item>\n                          <jats:p>Six SNPs identified that can characterize all haplotypes present at SD1 locus in diverse rice.<\/jats:p>\n                        <\/jats:list-item>\n                        <jats:list-item>\n                          <jats:p>\n                            Three alleles of the\n                            <jats:italic>SD1<\/jats:italic>\n                            gene identified in US rice germplasm including two semidwarf alleles.\n                          <\/jats:p>\n                        <\/jats:list-item>\n                        <jats:list-item>\n                          <jats:p>Two SNPs identified and validated that differentiate the SD1 allele present in US germplasm.<\/jats:p>\n                        <\/jats:list-item>\n                        <jats:list-item>\n                          <jats:p>KASP assays designed for both SNPs for use in high\u2010throughput breeding applications.<\/jats:p>\n                        <\/jats:list-item>\n                      <\/jats:list>\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:label\/>\n                    <jats:p>\n                      Plant height is an important target in US rice (\n                      <jats:italic>Oryza sativa<\/jats:italic>\n                      L.) breeding programs and the large effect of the\n                      <jats:italic>sd1<\/jats:italic>\n                      semidwarf gene makes it a suitable target for marker\u2010assisted selection. Although the deletion underlying the semidwarf allele is known and a gel\u2010based DNA marker is available, this marker is not ideal for applied breeding because of throughput and cost constraints. The objectives of this study were to characterize the haplotype diversity at the\n                      <jats:italic>SD1<\/jats:italic>\n                      locus within US rice germplasm and develop a single nucleotide polymorphism (SNP) assay for breeding applications. The International Rice Research Institute (IRRI) SNP\u2010Seek database was used to characterize the haplotype diversity present at the\n                      <jats:italic>SD1<\/jats:italic>\n                      locus across a set of rice accessions and seven haplotypes were identified. The US rice germplasm was not well represented in the IRRI database, so a set of six SNPs was identified that could differentiate all detected haplotypes. These SNPs were designed into Kompetitive allele specific polymerase chain reaction (KASP) assays and screened across 359 elite US genotypes. Of the seven haplotypes, two were present within the US germplasm, one of which was the semidwarf deletion allele. A third haplotype was observed within the US medium\u2010grain germplasm and demonstrated to be a semidwarf allele derived from the induced mutation in the \u2018Calrose76\u2019. Two SNPs were identified that distinguish the three\n                      <jats:italic>SD1<\/jats:italic>\n                      haplotypes present in the US germplasm. These SNPs were validated across the US germplasm and two biparental populations.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.3835\/plantgenome2019.02.0010","type":"journal-article","created":{"date-parts":[[2019,11,22]],"date-time":"2019-11-22T12:09:30Z","timestamp":1574424570000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":26,"title":["Haplotype Characterization of the\n                    <i>sd1<\/i>\n                    Semidwarf Gene in United States Rice"],"prefix":"10.1002","volume":"12","author":[{"given":"Brijesh","family":"Angira","sequence":"first","affiliation":[{"name":"H. Rouse Caffey Rice Research Station Louisiana State Univ. Agricultural Center 1373 Caffey Rd. Rayne LA 70578"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher K.","family":"Addison","sequence":"additional","affiliation":[{"name":"School of Plant, Environmental and Soil Science Louisiana State Univ. Baton Rouge LA 70808"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tommaso","family":"Cerioli","sequence":"additional","affiliation":[{"name":"School of Plant, Environmental and Soil Science Louisiana State Univ. Baton Rouge LA 70808"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Democrito B.","family":"Rebong","sequence":"additional","affiliation":[{"name":"School of Plant, Environmental and Soil Science Louisiana State Univ. Baton Rouge LA 70808"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Diane R.","family":"Wang","sequence":"additional","affiliation":[{"name":"Dep. of Geography Univ. at Buffalo Buffalo NY 14261"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nathan","family":"Pumplin","sequence":"additional","affiliation":[{"name":"Dep. of Plant Sciences Univ. of California\u2013Davis Davis CA 95616"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jong H.","family":"Ham","sequence":"additional","affiliation":[{"name":"Dep. of Plant Pathology and Crop Physiology Louisiana State Univ. Baton Rouge LA 70808"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James H.","family":"Oard","sequence":"additional","affiliation":[{"name":"H. Rouse Caffey Rice Research Station Louisiana State Univ. Agricultural Center 1373 Caffey Rd. Rayne LA 70578"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steven D.","family":"Linscombe","sequence":"additional","affiliation":[{"name":"H. Rouse Caffey Rice Research Station Louisiana State Univ. Agricultural Center 1373 Caffey Rd. Rayne LA 70578"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adam N.","family":"Famoso","sequence":"additional","affiliation":[{"name":"H. Rouse Caffey Rice Research Station Louisiana State Univ. Agricultural Center 1373 Caffey Rd. Rayne LA 70578"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2019,11]]},"reference":[{"key":"e_1_2_7_2_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku1039"},{"key":"e_1_2_7_3_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btm308"},{"key":"e_1_2_7_4_1","first-page":"77","volume-title":"Rice breeding","author":"Chandler R.","year":"1972"},{"key":"e_1_2_7_5_1","doi-asserted-by":"publisher","DOI":"10.2307\/1241374"},{"key":"e_1_2_7_6_1","doi-asserted-by":"publisher","DOI":"10.2134\/agronj1968.00021962006000060017x"},{"key":"e_1_2_7_7_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0124617"},{"key":"e_1_2_7_8_1","doi-asserted-by":"publisher","DOI":"10.1093\/database\/baw107"},{"key":"e_1_2_7_9_1","doi-asserted-by":"publisher","DOI":"10.1007\/978\u20101\u20104939\u20100446\u20104_7"},{"key":"e_1_2_7_10_1","first-page":"117","volume-title":"Rice research and production in the 21st century: Symposium honoring Robert F. 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