Fine mapping of a major QTL for flag leaf width in rice, qFLW4, which might be caused by alternative splicing of NAL1

Chen, Mingliang; Luo, Jianxun; Shao, Gaoneng; Wei, Xiangjin; Tang, Shaoqing; Sheng, Zhonghua; Song, Jian

doi:10.1007/s00299-011-1207-7

Cited by 61 publications

(40 citation statements)

References 43 publications

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“…Among these QTLs, 1 QTL on chromosome 8 controlling length, width, and flag leaf area was at the same location. Since then, QTL mapping for flag leaf traits has been extensively conducted in different types of genetic populations, such as near isogenic lines, backcross inbred lines, doubled haploids (DHs), and F 2 , with more than 100 QTLs identified (Dong et al, 2003;Kobayashi et al, 2003;Shen et al, 2003;Wang et al, 2004;Yue et al, 2006;Cao et al, 2007;Tong et al, 2007;Farooq et al, 2010;Ding et al, 2011;Wang et al, 2011;Sonah et al, 2012;Chen et al, 2012). For example, Kobayashi et al (2003) mapped QTLs for FLL, FLW, and FLA using the Milyang23/Akihikari RIL population over 5 seasons, and found a total of 9 genomic regions involved in leaf development.…”

Section: Introductionmentioning

confidence: 99%

QTLs for rice flag leaf traits in doubled haploid populations in different environments

et al. 2015

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ABSTRACT. Two rice doubled haploid (DH) populations derived from the crosses of ZYQ8/JX17 and CJ06/TN1 were used to detect quantitative trait loci (QTLs) for flag leaf length (FLL), width (FLW), and angle (FLA) under long-day conditions in Hangzhou (subtropical zone) and short-day conditions in Hainan (tropical zone), China. The four parents differed significantly in all 3 traits. FLL was found to be positively correlated with FLW in the 2 populations. A total of 30 QTLs were identified for flag leaf traits, with a contribution to the phenotypic variation of each QTL from 4.49 to 26.30%. Among these, qFLL-4b, qFLW-12, and qFLA-2a showed larger additive effects on the phenotype and explained more variations compared to the other QTLs. qFLL-1a and qFLL-8 were detected in both environments, while qFLL-2, qFLW11, qFLW2, and qFLA8 were novel QTLs, which may be beneficial to rice ideal-type breeding.

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Section: Introductionmentioning

confidence: 99%

QTLs for rice flag leaf traits in doubled haploid populations in different environments

et al. 2015

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“…However, it could not explain the results of Chen et al (2012), where the R-type allele increased WFL in mapping of QTL for WFL using hybrid populations originated from a cross between D50 (R-type allele) and HB277 (H-type allele). This discrepancy might be because of the presence of a large number of alternatively spliced forms of the H-type allele and a low level of the NAL1 protein (Chen et al 2012). However, further analyses are required to identify the exact reason for this discrepancy.…”

Section: Products Of the Malfunctional H 233 -Type Allele Still Regulmentioning

confidence: 92%

“…This would also explain the increase in WFL when the Daringan allele (H-type allele) was introduced into IR64 (R-type allele) (Fujita et al 2013) and when the Nipponbare allele (H-type allele) was introduced into 93-11 (R-type allele) (Zhang et al 2014). However, it could not explain the results of Chen et al (2012), where the R-type allele increased WFL in mapping of QTL for WFL using hybrid populations originated from a cross between D50 (R-type allele) and HB277 (H-type allele). This discrepancy might be because of the presence of a large number of alternatively spliced forms of the H-type allele and a low level of the NAL1 protein (Chen et al 2012).…”

Section: Products Of the Malfunctional H 233 -Type Allele Still Regulmentioning

confidence: 95%

“…It was reported that the H-type allele in HB277 but not the R-type allele in D50 was subject to extensive alternative splicing, while both were expressed at similar levels (Chen et al 2012). In Koshihikari (type VI9), only 20% of NAL1 transcripts contained no retrotransposon, and a NAL1 protein the same size as that encoded by the R-type allele was synthesized (Takai et al 2013).…”

Section: Amino Acid Change In Nal1 Is Important For Increased Wflmentioning

confidence: 99%

“…NAL1 was originally isolated as a gene affecting vascular patterns in a study on a classic dwarf mutant with a narrow leaf (Qi et al 2008) and was later shown to affect WFL, total spikelet number per panicle, photosynthetic rate, and chlorophyll content (Chen et al 2012;Fujita et al 2013;Takai et al 2013;Zhang et al 2014). NAL1 encodes a plant-specific protein, and the nal1 mutant with an in-frame deletion of 10 amino acids in exon 4 showed reduced basipetal polar auxin transport and fewer longitudinal veins, compared with wild type (Qi et al 2008).…”

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confidence: 99%

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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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Prototype for developing SNP markers from GWAS and biparental QTL for rice panicle and grain traits

Eizenga

Jackson

Edwards

2021

Agricultural & Env Letters

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There is a large gap between genomewide association studies (GWAS) and developing markers that can be used in marker-assisted selection (MAS) schemes for cultivar improvement. This study is a prototype for developing markers using segregating single nucleotide polymorphisms (SNPs) for panicle architecture and grain shape traits identified by GWAS in the Rice Diversity Panel-1 and colocalized in QTL regions revealed by linkage mapping in the Estrela × NSFTV199 rice (Oryza sativa L.) population. Markers were developed from sequence variants suitable for reliable detection in regions surrounding the most significant SNPs identified in GWAS. Once developed, the markers were validated in three Japonica subspecies biparental populations, used to improve QTL mapping resolution, and employed to select potential parents for use in MAS. All marker alleles segregated in the rice tropical japonica subpopulation.

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Fine mapping of a major QTL for flag leaf width in rice, qFLW4, which might be caused by alternative splicing of NAL1

Cited by 61 publications

References 43 publications

QTLs for rice flag leaf traits in doubled haploid populations in different environments

QTLs for rice flag leaf traits in doubled haploid populations in different environments

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

Prototype for developing SNP markers from GWAS and biparental QTL for rice panicle and grain traits

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