Uncovering of major genetic factors generating naturally occurring variation in heading date among Asian rice cultivars

Ebana, Kaworu; Shibaya, Taeko; Wu, Jianzhong; Matsubara, Kazuki; Kanamori, Hajime; Yamane, Hiroko; Yamanouchi, Utako; Mizubayashi, Tatsumi; Kono, Izumi; Shomura, Ayahiko; Ito, Sachie; Ando, Tsuyu; Hori, Kiyosumi; Matsumoto, Takashi; Yano, Masahiro

doi:10.1007/s00122-010-1524-1

Cited by 68 publications

(67 citation statements)

References 45 publications

(80 reference statements)

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“…However, it appears that prezygotic barriers do not intrinsically impair crossing among Asian rice cultivars, because they are easily crossed with one another (Chu et al 1969). Rather, geographical and temporal isolation (particularly variation in Xowering time; e.g., Ebana et al 2011) may be important prezygotic barriers in rice.…”

Section: Discussionmentioning

confidence: 93%

Relationship between transmission ratio distortion and genetic divergence in intraspecific rice crosses

et al. 2011

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The strength of reproductive isolation often correlates positively with parental divergence in both animals and plants. Here, we assess the relationship between transmission ratio distortion (TRD) of marker loci and parental divergence in intraspecific rice (Oryza sativa L.) crosses. We produced 10 diverse F(2) populations by crossing a temperate japonica reference accession with each of 10 donor accessions belonging to subpopulations different from the reference accession, and then genotyped the F(2) populations using molecular markers distributed across the entire genome. Significant TRDs (α = 0.05) were detected in 9 of the 10 F(2) populations. TRD regions on chromosomes 3 and 6 were common to several populations; in contrast, other TRD regions were unique to a single population, indicating the diversification of genomic location of TRDs among the populations. The level of TRD (estimated from the overall number and magnitude of TRDs) was significantly correlated with the genetic distance between the donor accessions and the reference accession. Our results suggest that in intraspecific rice crosses, parental divergence may result in diversification of the TRD pattern, followed by an increase in the level of TRD.

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Section: Discussionmentioning

confidence: 93%

Relationship between transmission ratio distortion and genetic divergence in intraspecific rice crosses

et al. 2011

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“…In rice, polymorphism in Hd1 protein, the type of Hd3a promoter and the level of Ehd1 expression were related to diversity of flowering time and geographic adaptation in cultivated rice species (66). Ebana et al (67) found that functional polymorphisms in several identified key genes (Hd1, RFT1, and Ghd7) contributed greatly to the diversity of rice heading dates. Table S2).…”

Section: E1 Locus Was Delimited To a 174-kb Region That Contained A mentioning

confidence: 99%

Positional cloning and characterization reveal the molecular basis for soybean maturity locus E1 that regulates photoperiodic flowering

Xia

Watanabe

Yamada

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

389

551

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The complex and coordinated regulation of flowering has high ecological and agricultural significance. The maturity locus E1 has a large impact on flowering time in soybean, but the molecular basis for the E1 locus is largely unknown. Through positional cloning, we delimited the E1 locus to a 17.4-kb region containing an intron-free gene (E1). The E1 protein contains a putative bipartite nuclear localization signal and a region distantly related to B3 domain. In the recessive allele, a nonsynonymous substitution occurred in the putative nuclear localization signal, leading to the loss of localization specificity of the E1 protein and earlier flowering. The early-flowering phenotype was consistently observed in three ethylmethanesulfonate-induced mutants and two natural mutations that harbored a premature stop codon or a deletion of the entire E1 gene. E1 expression was significantly suppressed under short-day conditions and showed a bimodal diurnal pattern under long-day conditions, suggesting its response to photoperiod and its dominant effect induced by long day length. When a functional E1 gene was transformed into the early-flowering cultivar Kariyutaka with low E1 expression, transgenic plants carrying exogenous E1 displayed late flowering. Furthermore, the transcript abundance of E1 was negatively correlated with that of GmFT2a and GmFT5a, homologues of FLOWERING LOCUS T that promote flowering. These findings demonstrated the key role of E1 in repressing flowering and delaying maturity in soybean. The molecular identification of the maturity locus E1 will contribute to our understanding of the molecular mechanisms by which a short-day plant regulates flowering time and maturity. photoperiodism | quantitative trait locus | photoperiodic insensibility

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“…The SSR markers were selected from those described in McCouch et al (2002) and the International Rice Genome Sequencing Project (2005). Polymorphisms were detected as described by Ebana et al (2011). Genomic DNA was extracted from leaves of each plant by the cetyl trimethylammonium bromide method.…”

Section: Quantitative Trait Loci Analysismentioning

confidence: 99%

Natural Variation in the Flag Leaf Morphology of Rice Due to a Mutation of the NARROW LEAF 1 Gene in Oryza sativa L.

et al. 2015

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We investigated the natural variations in the flag leaf morphology of rice. We conducted a principal component analysis based on nine flag leaf morphology traits using 103 accessions from the National Institute of Agrobiological Sciences Core Collection. The first component explained 39% of total variance, and the variable with highest loading was the width of the flag leaf (WFL). A genomewide association analysis of 102 diverse Japanese accessions revealed that marker RM6992 on chromosome 4 was highly associated with WFL. In analyses of progenies derived from a cross between Takanari and Akenohoshi, the most significant quantitative trait locus (QTL) for WFL was in a 10.3-kb region containing the NARROW LEAF 1 (NAL1) gene, located 0.4 Mb downstream of RM6992. Analyses of chromosomal segment substitution lines indicated that a mutation (G1509A single-nucleotide mutation, causing an R233H amino acid substitution in NAL1) was present at the QTL. This explained 13 and 20% of total variability in WFL and the distance between small vascular bundles, respectively. The mutation apparently occurred during rice domestication and spread into japonica, tropical japonica, and indica subgroups. Notably, one accession, Phulba, had a NAL1 allele encoding only the N-terminal, or one-fourth, of the wild-type peptide. Given that the Phulba allele and the histidine-type allele showed essentially the same phenotype, the histidine-type allele was regarded as malfunctional. The phenotypes of transgenic plants varied depending on the ratio of histidine-type alleles to arginine-type alleles, raising the possibility that H 233 -type products function differently from and compete with R 233 -type products.KEYWORDS rice; flag leaf width; natural variation; Oryza sativa L.; NARROW LEAF 1 T HE leaf of grasses typically consists of a relatively narrow blade and sheath enclosing the stem, and venation is parallel in the blade and the sheath (Esau 1977). Because large leaves intercept more light, the leaf area of the blade strongly affects final yield in cereal crops (Watson 1952). To produce plants that intercept light efficiently, leaf angle has been a target in breeding programs because erect leaves can capture more sunlight (Sinclair and Sheehy 1999). It was demonstrated that a brassinosteroid-deficient mutant with erect leaves showed increased grain yield under dense planting conditions (Sakamoto et al. 2005). It is also essential to understand the mechanism of development and the natural variations in morphology of the flag leaf since photosynthesis in the top three leaf blades of the plant, especially flag leaf, makes the largest contribution to the grain yield of rice (Tanaka 1958;Yoshida 1972). The developmental processes of the flag leaf are the same as those of other leaves. In rice, the longitudinal strands in the leaf comprise the midrib, large vascular bundles, and small vascular bundles (Hoshikawa 1989). According to Inosaka (1962) and Itoh et al. (2005), the midrib and large vascular bundles initiate at the base of the...

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Uncovering of major genetic factors generating naturally occurring variation in heading date among Asian rice cultivars

Cited by 68 publications

References 45 publications

Relationship between transmission ratio distortion and genetic divergence in intraspecific rice crosses

Relationship between transmission ratio distortion and genetic divergence in intraspecific rice crosses

Positional cloning and characterization reveal the molecular basis for soybean maturity locus E1 that regulates photoperiodic flowering

Natural Variation in the Flag Leaf Morphology of Rice Due to a Mutation of the NARROW LEAF 1 Gene in Oryza sativa L.

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