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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.

ABSTRACT: 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 ? 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.

SUBMITTER: Rebolledo MC

PROVIDER: S-EPMC5029283 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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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.

Rebolledo Maria C MC Peña Alexandra L AL Duitama Jorge J Cruz Daniel F DF Dingkuhn Michael M Grenier Cecile C Tohme Joe J

Frontiers in plant science 20160920

Number of spikelets per panicle (NSP) is a key trait to increase yield potential in rice (<i>O. sativa</i>). 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) th ...[more]

PMID: 27703460

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Project description:BackgroundRice (Oryza sativa L.) is a staple food crop worldwide. Its yield and quality are affected by its tillering pattern and spikelet development. Although many genes involved in the vegetative and reproductive development of rice have been characterized in previous studies, the genetic mechanisms that control axillary tillering, spikelet development, and panicle exsertion remain incompletely understood.ResultsHere, we characterized a novel rice recombinant inbred line (RIL), panicle exsertion defect and aberrant spikelet (pds). It was derived from a cross between two indica varieties, S142 and 430. Intriguingly, no abnormal phenotypes were observed in the parents of pds. This RIL exhibited sheathed panicles at heading stage. Still, a small number of tillers in pds plants were fully exserted from the flag leaves. Elongated sterile lemmas and rudimentary glumes (occurred occasionally) were observed in the spikelets of the exserted panicles and were transformed into palea/lemma-like structures. Furthermore, more interestingly, tillers occasionally grew from the axils of the elongated rudimentary glumes. Via genetic linkage analysis, we found that the abnormal phenotype of pds manifesting as genetic incompatibility or hybrid weakness was caused by genetic interaction between a recessive locus, pds1, which was derived from S142 and mapped to chromosome 8, and a locus pds2, which not yet mapped from 430. We fine-mapped pds1 to an approximately 55-kb interval delimited by the markers pds-4 and 8 M3.51. Six RGAP-annotated ORFs were included in this genomic region. qPCR analysis revealed that Loc_Os080595 might be the target of pds1 locus, and G1 gene might be involved in the genetic mechanism underlying the pds phenotype.ConclusionsIn this study, histological and genetic analyses revealed that the pyramided pds loci resulted in genetic incompatibility or hybrid weakness in rice might be caused by a genetic interaction between pds loci derived from different rice varieties. Further isolation of pds1 and its interactor pds2, would provide new insight into the molecular regulation of grass inflorescence development and exsertion, and the evolution history of the extant rice.

Dataset Information

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.

Publications

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.

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