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Fu C.-Y.,Guangdong Academy of Agricultural Sciences | Fu C.-Y.,Guangdong Provincial Key Laboratory of New Technology in Rice Breeding | Wang F.,Guangdong Academy of Agricultural Sciences | Wang F.,Guangdong Provincial Key Laboratory of New Technology in Rice Breeding | And 17 more authors.
PLoS ONE | Year: 2013

Hybrid weakness (HW) is an important postzygotic isolation which occurs in both intra- and inter-specific crosses. In this study, we described a novel low temperature-dependent intrasubspecific hybrid weakness in the F1 plants derived from the cross between two indica rice varieties Taifeng A and V1134. HW plants showed growth retardation, reduced panicle number and pale green leaves with chlorotic spots. Cytological assay showed that there were reduced cell numbers, larger intercellular spaces, thicker cell walls, and abnormal development of chloroplast and mitochondria in the mature leaves from HW F1 plants in comparison with that from both of the parental lines. Genetic analysis revealed that HW was controlled by two complementary dominant genes Hw3 from V1134 and Hw4 from Taifeng A. Hw3 was mapped in a 136 kb interval between the markers Indel1118 and Indel1117 on chromosome 11, and Hw4 was mapped in the region of about 15 cM between RM182 and RM505 on chromosome 7, respectively. RT-PCR analysis revealed that only LOC_Os11g44310, encoding a putative calmodulin-binding protein (OsCaMBP), differentially expressed among Taifeng A, V1134 and their HW F1. No recombinant was detected using the markers designed based on the sequence of LOC_Os11g44310 in the BC1F2 (Taifeng A//Taifeng A/V1134) population. Hence, LOC_Os11g44310 was probably the candidate gene of Hw3. Gene amplification suggested that LOC_Os11g44310 was present in V1134 and absent in Taifeng A. BLAST search revealed that LOC_Os11g44310 had one copy in the japonica genomic sequence of Nipponbare, and no homologous sequence in the indica reference sequence of 9311. Our results indicate that Hw3 is a novel gene for inducing hybrid weakness in rice. © 2013 Fu et al. Source

Liu D.,Guangdong Academy of Agricultural Sciences | Liu D.,Guangdong Provincial Key Laboratory of New Technology in Rice Breeding | Kang M.,Guangdong Academy of Agricultural Sciences | Kang M.,Guangdong Provincial Key Laboratory of New Technology in Rice Breeding | And 19 more authors.
Euphytica | Year: 2015

Grain size is a major component of rice grain yield and grain quality. Here we conducted genetic analysis for grain size using an F8 recombinant inbred lines population derived from the cross between two elite indica parents, the slender-grain line Taifeng B with good grain quality and the high-yielding short-grain cultivar Tesanai 2. Strong positive association between hundred-grain weight and grain width was observed, but significant negative correlation was found between grain length and grain width. A total of 36 QTLs for grain weight, grain length, grain width, grain length/width ratio and grain thickness were identified and they explained a total phenotypic variance ranging from 53.6 to 75.2 %. Of them, 6 QTLs were reported for the first time and they are likely novel genetic loci. Moreover, QTLs for grain size tend to form clusters at similar locations. Three of them were detected on chromosome 3, 5, and 7, locating at the regions of the previously reported loci GS3, qSW5/GW5 and GS7, respectively. The allele variance of the above three loci between the parental lines was verified by using functional marker and genome re-sequencing. The major QTLs and QTL clusters discovered in this study are valuable for improvement of rice grain yield and quality through marker-assisted selection. The repeatedly detected QTLs and newly identified loci lay foundation for further fine mapping and map-based cloning. © 2015 Springer Science+Business Media Dordrecht Source

Fu C.-Y.,Guangdong Academy of Agricultural Sciences | Fu C.-Y.,Guangdong Provincial Key Laboratory of New Technology in Rice Breeding | Liu W.-G.,Guangdong Academy of Agricultural Sciences | Liu W.-G.,Guangdong Provincial Key Laboratory of New Technology in Rice Breeding | And 14 more authors.
Genome | Year: 2016

Next-generation sequencing technologies provide opportunities to further understand genetic variation, even within closely related cultivars. We performed whole genome resequencing of two elite indica rice varieties, RGD-7S and Taifeng B, whose F1 progeny showed hybrid weakness and hybrid vigor when grown in the early-and late-cropping seasons, respectively. Approximately 150 million 100-bp pair-end reads were generated, which covered ∼86% of the rice (Oryza sativa L. japonica 'Nipponbare') reference genome. A total of 2 758 740 polymorphic sites including 2 408 845 SNPs and 349 895 InDels were detected in RGD-7S and Taifeng B, respectively. Applying stringent parameters, we identified 961 791 SNPs and 46 640 InDels between RGD-7S and Taifeng B (RGD-7S/Taifeng B). The density of DNA polymorphisms was 256.8 SNPs and 12.5 InDels per 100 kb for RGD-7S/Taifeng B. Copy number variations (CNVs) were also investigated. In RGD-7S, 1989 of 2727 CNVs were overlapped in 218 genes, and 1231 of 2010 CNVs were annotated in 175 genes in Taifeng B. In addition, we verified a subset of InDels in the interval of hybrid weakness genes, Hw3 and Hw4, and obtained some polymorphic InDel markers, which will provide a sound foundation for cloning hybrid weakness genes. Analysis of genomic variations will also contribute to understanding the genetic basis of hybrid weakness and heterosis. © 2016 Published by NRC Research Press. Source

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