Identification of a candidate gene for panicle length in rice (Oryza sativa L.) via association and linkage analysis
Panicle length (PL) is an important trait for improving panicle architecture and grain yield in rice (Oryza sativa L.). Three populations were used to identify QTLs and candidate genes associated with PL. Four QTLs for PL were detected on chromosomes 4, 6 and 9 through linkage mapping in the recombi...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2016-05-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fpls.2016.00596/full |
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| author | Erbao eLiu Yang eLiu Guocan eWu Siyuan eZeng Tran Thi eTran Thi Lijun eLiang Zhiyao eDong Yinfeng eLiang Dong eShe Hui eWang Imdad Ullan eZaid Delin eHong |
| author_facet | Erbao eLiu Yang eLiu Guocan eWu Siyuan eZeng Tran Thi eTran Thi Lijun eLiang Zhiyao eDong Yinfeng eLiang Dong eShe Hui eWang Imdad Ullan eZaid Delin eHong |
| author_sort | Erbao eLiu |
| collection | DOAJ |
| description | Panicle length (PL) is an important trait for improving panicle architecture and grain yield in rice (Oryza sativa L.). Three populations were used to identify QTLs and candidate genes associated with PL. Four QTLs for PL were detected on chromosomes 4, 6 and 9 through linkage mapping in the recombinant inbred line population derived from a cross between the cultivars Xiushui79 (short panicle) and C-bao (long panicle). Ten SSR markers associated with PL were detected on chromosomes 2, 3, 5, 6, 8, 9 and 10 in the natural population consisting of 540 accessions collected from East and Southeast Asia. A major locus on chromosome 9 with the largest effect was identified via both linkage and association mapping. LONG PANICLE 1 (LP1) locus was delimited to a 90-kb region of the long arm of chromosome 9 through fine mapping using a single segment segregating F2 population. Two single nucleotide polymorphisms (SNPs) leading to amino acid changes were detected in the third and fifth exons of LP1. LP1encodes a Remorin_C-containing protein of unknown function with homologs in a variety of species. Sequencing analysis of LP1 in two parents and 103 rice accessions indicated that SNP1 is associated with panicle length. The LP1 allele of Xiushui79 leads to reduced panicle length, whereas the allele of C-bao relieves the suppression of panicle length. LP1 and the elite alleles can be used to improve panicle length in rice. |
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| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-18T08:28:57Z |
| publishDate | 2016-05-01 |
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| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-11fd48dcd68f4ab3ac2a30720a7ae79d2022-12-21T21:14:31ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2016-05-01710.3389/fpls.2016.00596195360Identification of a candidate gene for panicle length in rice (Oryza sativa L.) via association and linkage analysisErbao eLiu0Yang eLiu1Guocan eWu2Siyuan eZeng3Tran Thi eTran Thi4Lijun eLiang5Zhiyao eDong6Yinfeng eLiang7Dong eShe8Hui eWang9Imdad Ullan eZaid10Delin eHong11Nanjing Agricultural UniversityNanjing Agricultural UniversityNanjing Agricultural UniversityNanjing Agricultural UniversityNanjing Agricultural UniversityNanjing Agricultural UniversityNanjing Agricultural UniversityNanjing Agricultural UniversityNanjing Agricultural UniversityNanjing Agricultural UniversityNanjing Agricultural UniversityNanjing Agricultural UniversityPanicle length (PL) is an important trait for improving panicle architecture and grain yield in rice (Oryza sativa L.). Three populations were used to identify QTLs and candidate genes associated with PL. Four QTLs for PL were detected on chromosomes 4, 6 and 9 through linkage mapping in the recombinant inbred line population derived from a cross between the cultivars Xiushui79 (short panicle) and C-bao (long panicle). Ten SSR markers associated with PL were detected on chromosomes 2, 3, 5, 6, 8, 9 and 10 in the natural population consisting of 540 accessions collected from East and Southeast Asia. A major locus on chromosome 9 with the largest effect was identified via both linkage and association mapping. LONG PANICLE 1 (LP1) locus was delimited to a 90-kb region of the long arm of chromosome 9 through fine mapping using a single segment segregating F2 population. Two single nucleotide polymorphisms (SNPs) leading to amino acid changes were detected in the third and fifth exons of LP1. LP1encodes a Remorin_C-containing protein of unknown function with homologs in a variety of species. Sequencing analysis of LP1 in two parents and 103 rice accessions indicated that SNP1 is associated with panicle length. The LP1 allele of Xiushui79 leads to reduced panicle length, whereas the allele of C-bao relieves the suppression of panicle length. LP1 and the elite alleles can be used to improve panicle length in rice.http://journal.frontiersin.org/Journal/10.3389/fpls.2016.00596/fullriceassociation analysisgene identificationquantitative trait locusmap-based cloningPanicle length |
| spellingShingle | Erbao eLiu Yang eLiu Guocan eWu Siyuan eZeng Tran Thi eTran Thi Lijun eLiang Zhiyao eDong Yinfeng eLiang Dong eShe Hui eWang Imdad Ullan eZaid Delin eHong Identification of a candidate gene for panicle length in rice (Oryza sativa L.) via association and linkage analysis Frontiers in Plant Science rice association analysis gene identification quantitative trait locus map-based cloning Panicle length |
| title | Identification of a candidate gene for panicle length in rice (Oryza sativa L.) via association and linkage analysis |
| title_full | Identification of a candidate gene for panicle length in rice (Oryza sativa L.) via association and linkage analysis |
| title_fullStr | Identification of a candidate gene for panicle length in rice (Oryza sativa L.) via association and linkage analysis |
| title_full_unstemmed | Identification of a candidate gene for panicle length in rice (Oryza sativa L.) via association and linkage analysis |
| title_short | Identification of a candidate gene for panicle length in rice (Oryza sativa L.) via association and linkage analysis |
| title_sort | identification of a candidate gene for panicle length in rice oryza sativa l via association and linkage analysis |
| topic | rice association analysis gene identification quantitative trait locus map-based cloning Panicle length |
| url | http://journal.frontiersin.org/Journal/10.3389/fpls.2016.00596/full |
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