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Identification and characterization of stable QTLs for vascular bundle number at the panicle neck in rice (Oryza sativa L.).

ABSTRACT: A large vascular bundle number (VBN) in the panicle neck in rice (Oryza sativa L.) is related to the ability to transport assimilates from stem and leaf to reproductive organs during seed maturation. Several quantitative trait loci (QTLs) for VBN have been identified by using segregating populations derived from a cross between indica and japonica rice cultivars. However, the detailed location, effect, and interaction of QTLs for VBN were not understood well. Here, to elucidate the genetic basis of VBN, we identified three stable QTLs for VBN-qVBN5, qVBN6 and qVBN11-by using 71 recombinant inbred lines derived from a cross between indica 'IR24' and japonica 'Asominori'. We confirmed their positions and characterized their effects by using chromosome segment substitution lines (CSSLs) with an 'IR24' genetic background. qVBN6 had the most substantial effect on VBN, followed by qVBN11 and qVBN5. We developed pyramided lines carrying two QTLs for VBN to estimate their interaction. The combination of qVBN6 and qVBN11 accumulated VBN negatively in the pyramided lines owing to the independent actions of each QTL. The QTLs detected for VBN will enhance our understanding of genetic mechanisms of VBN and can be used in rice breeding.

SUBMITTER: Nguyen HTL

PROVIDER: S-EPMC10722095 | biostudies-literature | 2023 Sep

REPOSITORIES: biostudies-literature

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Identification and characterization of stable QTLs for vascular bundle number at the panicle neck in rice (Oryza sativa L.).

Nguyen Ha Thi Le HTL Suetsugu Shizuka S Nakamura Yuna Y Demeter Zita Z Zheng Shao-Hui SH Fujita Daisuke D

Breeding science 20230909 4

A large vascular bundle number (VBN) in the panicle neck in rice (Oryza sativa L.) is related to the ability to transport assimilates from stem and leaf to reproductive organs during seed maturation. Several quantitative trait loci (QTLs) for VBN have been identified by using segregating populations derived from a cross between indica and japonica rice cultivars. However, the detailed location, effect, and interaction of QTLs for VBN were not understood well. Here, to elucid ...[more]

PMID: 38106512

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Project description:BackgroundDeveloping high yielding varieties is a major challenge for breeders tackling the challenges of climate change in agriculture. The panicle (inflorescence) architecture of rice is one of the key components of yield potential and displays high inter- and intra-specific variability. The genus Oryza features two different crop species: Asian rice (Oryza sativa L.) and the African rice (O. glaberrima Steud.). One of the main morphological differences between the two independently domesticated species is the structure (or complexity) of the panicle, with O. sativa displaying a highly branched panicle, which in turn produces a larger number of grains than that of O. glaberrima. The gene regulatory network that governs intra- and interspecific panicle diversity is still under-studied.ResultsTo identify genetic factors linked to panicle architecture diversity in the two species, we used a set of 60 Chromosome Segment Substitution Lines (CSSLs) issued from third generation backcross (BC3DH) and carrying genomic segments from O. glaberrima cv. MG12 in the genetic background of O. sativa Tropical Japonica cv. Caiapó. Phenotypic data were collected for rachis and primary branch length, primary, secondary and tertiary branch number and spikelet number. A total of 15 QTLs were localized on chromosomes 1, 2, 3, 7, 11 and 12, QTLs associated with enhanced secondary and tertiary branch numbers were detected in two CSSLs. Furthermore, BC4F3:5 lines carrying different combinations of substituted segments were produced to decipher the effects of the identified QTL regions on variations in panicle architecture. A detailed analysis of phenotypes versus genotypes was carried out between the two parental genomes within these regions in order to understand how O. glaberrima introgression events may lead to alterations in panicle traits.ConclusionOur analysis led to the detection of genomic variations between O. sativa cv. Caiapó and O. glaberrima cv. MG12 in regions associated with enhanced panicle traits in specific CSSLs. These regions contain a number of key genes that regulate panicle development in O. sativa and their interspecific genomic variations may explain the phenotypic effects observed.

Project description:BackgroundFlag leaf (FL) and panicle architecture (PA) are critical for increasing rice grain yield as well as production. A genome-wide association study (GWAS) can better understand the genetic pathways behind complex traits like FL and PA.ResultsIn this study, 208 diverse rice germplasms were grown in the field at the Texas A&M AgriLife Research Center at Beaumont, TX, during 2022 and 2023 following Augmented Randomized Complete Block Design. After heading, eight different flag leaf and panicle architecture (FLPA) related traits were measured. GWAS analyses were performed to identify potential genomic regions associated with FLPA traits. A total of 97 quantitative trait loci (QTLs) (48 in 2022 and 49 in 2023) were distributed across all 12 chromosomes. GWAS revealed four QTLs (qSBPP4-2, qFLW6-2, qGNPP9, and qGWPP2-3) with phenotypic variation ranging from 11.7 to 22.3%. Two genetic loci were identified as multi-trait QTLs, i.e., S04_32100268 (qFLL4-1 and qFLA4-1) and S04_11552936 (qFLW4 and qFLA4-2) during 2022 and 2023, respectively. Additionally, these loci were further utilized to analyze candidate genes, and 65 genes were predicted in the 100-kb genomic region upstream and downstream. In silico expression analysis revealed 15 genes were expressed during the reproductive stage. These genes were associated with protein kinase, heat shock transcription factor family, sugar transporter conserved site and transcription factor bHLH95- like basic helix-loop-helix domain protein, as well as those that regulate the FLPA-related traits. Os04g0631100 was identified as a potential candidate gene that is highly expressed during the endosperm development stage, and it is associated with an important sugar transporter protein that will be helpful in grain improvement.ConclusionGWAS results revealed four major and two multi-trait QTLs. Expanding their candidate genes, and expression analysis provide the genetic information for molecular improvement of the FLPA-related trait in rice breeding programs.

Project description:BackgroundRice (Oryza sativa L.) yield is seriously influenced by panicle exsertion (PE) and the uppermost internode (UI) through panicle enclosure or energy transport during grain-filling stages. We evaluated the traits of PE and UI of 205 rice accessions in two independent environments and performed genome-wide association (GWAS) to explore the key genes controlling PE and UI, which could be used to improve panicle enclosure in rice breeding.ResultsIn this study, extensive genetic variation was found in both PE and UI among the 205 rice accessions, and 10.7% of accessions had panicle enclosure (PE/UI ≤ 0). Correlation analysis revealed that PE was significantly positively correlated with 1000-grain weight (1000-GW) but negatively correlated with heading date (HD), and UI was significantly positively correlated with HD but no significantly correlated with 1000-GW. A total of 22 and 24 quantitative trait loci (QTLs) were identified for PE and UI using GWAS, respectively. Eight loci for PE and nine loci for UI were simultaneously detected both in 2015 and in 2016, seven loci had adjacent physical positions between PE and UI, and ten loci for PE and seven loci for UI were located in previously reported QTLs. Further, we identified the CYP734A4 gene, encoding a cytochrome P450 monooxygenase, and the OsLIS-L1 gene, encoding a lissencephaly type-1-like protein, as causal genes for qPE14 and qUI14, and for qPE19, respectively. PE and UI were both significantly shorter in these two genes' mutants than in WT. Allelic Hap.1/2/4 of CYP734A4 and Hap.1/2/4 of OsLIS-L1 increased PE, UI, PE/UI, and 1000-GW, but Hap.3 of CYP734A4 and Hap.3 of OsLIS-L1 reduced them. In addition, six candidate genes were also detected for four key novel loci, qPE16, qPE21, qUI1, and qUI18, that seemed to be related to PE and UI.ConclusionsOur results provide new information on the genetic architecture of PE and UI in rice, confirming that the CYP734A4 and OsLIS-L1 genes participate in PE and UI regulation, which could improve our understanding of the regulatory mechanism of PE and UI for rice breeding in the future.

Dataset Information

Identification and characterization of stable QTLs for vascular bundle number at the panicle neck in rice (Oryza sativa L.).

Publications

Identification and characterization of stable QTLs for vascular bundle number at the panicle neck in rice (<i>Oryza sativa</i> L.).

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