Combining image analysis, genome wide association studies and different field trials to reveal stable genetic regions related to panicle architecture and the number of spikelets per panicle in rice
Number of spikelets per panicle (NSP) is a key trait to increase yield potential in rice (O. sativa). The architecture of the rice inflorescence which is mainly determined by the length and number of primary (PBL and PBN) and secondary (SBL and SBN) branches can influence NSP. Although several genes...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2016-09-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fpls.2016.01384/full |
| _version_ | 1831695807833702400 |
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| author | Maria Camila Rebolledo Alexandra Lorena Pena Jorge Duitama Daniel Cruz michael Dingkuhn Cecile Grenier Cecile Grenier Joseph Tohme |
| author_facet | Maria Camila Rebolledo Alexandra Lorena Pena Jorge Duitama Daniel Cruz michael Dingkuhn Cecile Grenier Cecile Grenier Joseph Tohme |
| author_sort | Maria Camila Rebolledo |
| collection | DOAJ |
| description | Number of spikelets per panicle (NSP) is a key trait to increase yield potential in rice (O. sativa). The architecture of the rice inflorescence which is mainly determined by the length and number of primary (PBL and PBN) and secondary (SBL and SBN) branches can influence NSP. Although several genes controlling panicle architecture and NSP in rice have been identified, there is little evidence of (i) the genetic control of panicle architecture and NSP in different environments and (ii) the presence of stable genetic associations with panicle architecture across environments. This study combines image phenotyping of 225 accessions belonging to a genetic diversity array of indica rice grown under irrigated field condition in two different environments and Genome Wide Association Studies (GWAS) based on the genotyping of the diversity panel, providing 83,374 SNPs.Accessions sown under direct seeding in one environement had reduced Panicle Length (PL), NSP, PBN, PBL, SBN and SBL compared to those established under transplanting in the second environment. Across environments, NSP was significantly and positively correlated with PBN, SBN and PBL. However, the length of branches (PBL and SBL) was not significantly correlated with variables related to number of branches (PBN and SBN ), suggesting independent genetic control.Twenty- three GWAS sites were detected with P-values ≤ 1.0E-04 and 27 GWAS sites with p ≤ 5.9E-04. We found 17 GWAS sites related to NSP, 10 for PBN and 11 for SBN, 7 for PBL and 11 for SBL. This study revealed new regions related to NSP, but only three associations were related to both branching number (PBN and SBN) and NSP. Two GWAS sites associated with SBL and SBN were stable across contrasting environments and were not related to genes previously reported.The new regions reported in this study can help improving NSP in rice for both direct seeded and transplanted conditions. The integrated approach of high-throughput phenotyping, multi-environment field trials and GWAS has the potential to dissect complex traits, such as NSP, into less complex traits and to match single nucleotide polymorphisms with relevant function under different environments, offering a potential use for molecular breeding. |
| first_indexed | 2024-12-20T13:01:20Z |
| format | Article |
| id | doaj.art-2aeb02a4b4924ad1a0de956726c98b15 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-20T13:01:20Z |
| publishDate | 2016-09-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Plant Science |
| spelling | doaj.art-2aeb02a4b4924ad1a0de956726c98b152022-12-21T19:39:54ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2016-09-01710.3389/fpls.2016.01384207616Combining image analysis, genome wide association studies and different field trials to reveal stable genetic regions related to panicle architecture and the number of spikelets per panicle in riceMaria Camila Rebolledo0Alexandra Lorena Pena1Jorge Duitama2Daniel Cruz3michael Dingkuhn4Cecile Grenier5Cecile Grenier6Joseph Tohme7International Center for Tropical Agriculture CIATInternational Center for Tropical Agriculture CIATInternational Center for Tropical Agriculture CIATInternational Center for Tropical Agriculture CIATAgricultural Research for Development - CIRADAgricultural Research for Development - CIRADInternational Center for Tropical Agriculture CIATInternational Center for Tropical Agriculture CIATNumber of spikelets per panicle (NSP) is a key trait to increase yield potential in rice (O. sativa). The architecture of the rice inflorescence which is mainly determined by the length and number of primary (PBL and PBN) and secondary (SBL and SBN) branches can influence NSP. Although several genes controlling panicle architecture and NSP in rice have been identified, there is little evidence of (i) the genetic control of panicle architecture and NSP in different environments and (ii) the presence of stable genetic associations with panicle architecture across environments. This study combines image phenotyping of 225 accessions belonging to a genetic diversity array of indica rice grown under irrigated field condition in two different environments and Genome Wide Association Studies (GWAS) based on the genotyping of the diversity panel, providing 83,374 SNPs.Accessions sown under direct seeding in one environement had reduced Panicle Length (PL), NSP, PBN, PBL, SBN and SBL compared to those established under transplanting in the second environment. Across environments, NSP was significantly and positively correlated with PBN, SBN and PBL. However, the length of branches (PBL and SBL) was not significantly correlated with variables related to number of branches (PBN and SBN ), suggesting independent genetic control.Twenty- three GWAS sites were detected with P-values ≤ 1.0E-04 and 27 GWAS sites with p ≤ 5.9E-04. We found 17 GWAS sites related to NSP, 10 for PBN and 11 for SBN, 7 for PBL and 11 for SBL. This study revealed new regions related to NSP, but only three associations were related to both branching number (PBN and SBN) and NSP. Two GWAS sites associated with SBL and SBN were stable across contrasting environments and were not related to genes previously reported.The new regions reported in this study can help improving NSP in rice for both direct seeded and transplanted conditions. The integrated approach of high-throughput phenotyping, multi-environment field trials and GWAS has the potential to dissect complex traits, such as NSP, into less complex traits and to match single nucleotide polymorphisms with relevant function under different environments, offering a potential use for molecular breeding.http://journal.frontiersin.org/Journal/10.3389/fpls.2016.01384/fullGWASyieldriceimage analysisDirect seedinginflorescence architecture |
| spellingShingle | Maria Camila Rebolledo Alexandra Lorena Pena Jorge Duitama Daniel Cruz michael Dingkuhn Cecile Grenier Cecile Grenier Joseph Tohme Combining image analysis, genome wide association studies and different field trials to reveal stable genetic regions related to panicle architecture and the number of spikelets per panicle in rice Frontiers in Plant Science GWAS yield rice image analysis Direct seeding inflorescence architecture |
| title | Combining image analysis, genome wide association studies and different field trials to reveal stable genetic regions related to panicle architecture and the number of spikelets per panicle in rice |
| title_full | Combining image analysis, genome wide association studies and different field trials to reveal stable genetic regions related to panicle architecture and the number of spikelets per panicle in rice |
| title_fullStr | Combining image analysis, genome wide association studies and different field trials to reveal stable genetic regions related to panicle architecture and the number of spikelets per panicle in rice |
| title_full_unstemmed | Combining image analysis, genome wide association studies and different field trials to reveal stable genetic regions related to panicle architecture and the number of spikelets per panicle in rice |
| title_short | Combining image analysis, genome wide association studies and different field trials to reveal stable genetic regions related to panicle architecture and the number of spikelets per panicle in rice |
| title_sort | combining image analysis genome wide association studies and different field trials to reveal stable genetic regions related to panicle architecture and the number of spikelets per panicle in rice |
| topic | GWAS yield rice image analysis Direct seeding inflorescence architecture |
| url | http://journal.frontiersin.org/Journal/10.3389/fpls.2016.01384/full |
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