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Kazuhiro Sato - One of the best experts on this subject based on the ideXlab platform.
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mitochondrial genome sequences from wild and cultivated barley Hordeum Vulgare
BMC Genomics, 2016Co-Authors: Hiroshi Hisano, Mai Tsujimura, Hideya Yoshida, Toru Terachi, Kazuhiro SatoAbstract:Sequencing analysis of mitochondrial genomes is important for understanding the evolution and genome structures of various plant species. Barley is a self-pollinated diploid plant with seven chromosomes comprising a large haploid genome of 5.1 Gbp. Wild barley (Hordeum Vulgare ssp. spontaneum) and cultivated barley (H. Vulgare ssp. Vulgare) have cross compatibility and closely related genomes, although a significant number of nucleotide polymorphisms have been reported between their genomes. We determined the complete nucleotide sequences of the mitochondrial genomes of wild and cultivated barley. Two independent circular maps of the 525,599 bp barley mitochondrial genome were constructed by de novo assembly of high-throughput sequencing reads of barley lines H602 and Haruna Nijo, with only three SNPs detected between haplotypes. These mitochondrial genomes contained 33 protein-coding genes, three ribosomal RNAs, 16 transfer RNAs, 188 new ORFs, six major repeat sequences and several types of transposable elements. Of the barley mitochondrial genome-encoded proteins, NAD6, NAD9 and RPS4 had unique structures among grass species. The mitochondrial genome of barley was similar to those of other grass species in terms of gene content, but the configuration of the genes was highly differentiated from that of other grass species. Mitochondrial genome sequencing is essential for annotating the barley nuclear genome; our mitochondrial sequencing identified a significant number of fragmented mitochondrial sequences in the reported nuclear genome sequences. Little polymorphism was detected in the barley mitochondrial genome sequences, which should be explored further to elucidate the evolution of barley.
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qtl analysis in recombinant chromosome substitution lines and doubled haploid lines derived from a cross between Hordeum Vulgare ssp Vulgare and Hordeum Vulgare ssp spontaneum
Molecular Breeding, 2005Co-Authors: Kiyosumi Hori, Kazuhiro Sato, Nami Nankaku, Kazuyoshi TakedaAbstract:Recombinant chromosome substitution lines (RCSLs) were developed in BC3 generation to introduce segments of a wild barley strain ‘H602’ (Hordeum Vulgare ssp. spontaneum) into a barley cultivar ‘Haruna Nijo’ (H. Vulgare ssp. Vulgare) genetic background. One hundred thirty four RCSLs were genotyped by 25 SSR and 60 EST markers, which were localized on a linkage map of doubled haploid lines (DHLs) derived from the same cross combination. Graphical genotyping revealed that the observed average substitution ratio of H602 segment (12.9%) agreed with the expected substitution ratio (12.5%), and a minimum set of 19 RCSLs represented the entire H602 genome. Phenotypes of five qualitative and nine quantitative traits were scored in both the RCSLs and DHLs. Five qualitative traits were localized as morphological markers on the linkage map of the DHLs, and these molecular markers were aligned on the respective chromosomal regions in the RCSLs. Simple and composite interval mapping procedures detected a total of 18 and 24 QTLs for nine qualitative traits on the RCSLs and DHLs, respectively. Several QTLs were localized at coincident or very close regions on both linkage maps. In spite of general inferior agronomic performances in wild barley, several H602 QTL alleles showed agronomically positive effects. These RCSLs should contribute to substitution of favorable alleles from wild barley into cultivated barley. These RCSLs are also available as sources of near isogenic lines, with which we can apply advanced genetic analysis methods such as isolation of QTLs and detection of epistatic interactions among QTLs.
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development and characterization of recombinant chromosome substitution lines rcsls using Hordeum Vulgare subsp spontaneum as a source of donor alleles in a Hordeum Vulgare subsp Vulgare background
Genome, 2003Co-Authors: Ivan Matus, Kazuhiro Sato, Ann Corey, Tanya Filichkin, Patrick M Hayes, M I Vales, J G Kling, Oscar Rieralizarazu, W Powell, Robbie WaughAbstract:The ancestor of barley (Hordeum Vulgare subsp. spontaneum) may be a source of novel alleles for crop improvement. We developed a set of recombinant chromosome substitution lines (RCSLs) using an accession of H. Vulgare subsp. spontaneum (Caesarea 26-24, from Israel) as the donor and Hordeum Vulgare subsp. Vulgare 'Harrington' (the North American malting quality standard) as the recurrent parent via two backcrosses to the recurrent parent, followed by six generations of selfing. Here we report (i) the genomic architecture of the RCSLs, as inferred by simple sequence repeat (SSR) markers, and (ii) the effects of H. Vulgare subsp. spontaneum genome segment introgressions in terms of three classes of phenotypes: inflorescence yield components, malting quality traits, and domestication traits. Significant differences among the RCSLs were detected for all phenotypes measured. The phenotypic effects of the introgressions were assessed using association analysis, and these were referenced to quantitative trait lo...
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differential al resistance and citrate secretion in barley Hordeum Vulgare l
Planta, 2003Co-Authors: Kazuhiro Sato, Zhuqing Zhao, Jian Feng, Kazuyoshi TakedaAbstract:While barley (Hordeum Vulgare L.) is the most sensitive species to Al toxicity among small-grain crops, variation in Al resistance between cultivars does exist. We examined the mechanism responsible for differential Al resistance in 21 barley varieties. Citrate was secreted from the roots in response to Al stress. A positive correlation between citrate secretion and Al resistance [(root elongation with Al)/(root elongation without Al)] and a negative correlation between citrate secretion and Al content of root apices, were obtained, suggesting that citrate secretion from the root apices plays an important role in excluding Al and thereby detoxifying Al. The Al-induced secretion of citrate was characterized using an Al-resistant variety (Sigurdkorn) and an Al-sensitive variety (Kearney). In Sigurdkorn, Al-induced secretion of citrate occurred within 20 min, and the secretion did not increase with increasing external Al concentration. The Al-induced citrate secretion ceased at low temperature (6 °C) and was inhibited by anion-channel inhibitors. Internal citrate content of root apices was increased by Al exposure in Sigurdkorn, but was not affected in Kearney. The activity of citrate synthase was unaffected by Al in both Al-resistant and Al-sensitive varieties. The secretion rate of organic acid anions from barley was the lowest among wheat, rye and triticale.
Kazuyoshi Takeda - One of the best experts on this subject based on the ideXlab platform.
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qtl analysis in recombinant chromosome substitution lines and doubled haploid lines derived from a cross between Hordeum Vulgare ssp Vulgare and Hordeum Vulgare ssp spontaneum
Molecular Breeding, 2005Co-Authors: Kiyosumi Hori, Kazuhiro Sato, Nami Nankaku, Kazuyoshi TakedaAbstract:Recombinant chromosome substitution lines (RCSLs) were developed in BC3 generation to introduce segments of a wild barley strain ‘H602’ (Hordeum Vulgare ssp. spontaneum) into a barley cultivar ‘Haruna Nijo’ (H. Vulgare ssp. Vulgare) genetic background. One hundred thirty four RCSLs were genotyped by 25 SSR and 60 EST markers, which were localized on a linkage map of doubled haploid lines (DHLs) derived from the same cross combination. Graphical genotyping revealed that the observed average substitution ratio of H602 segment (12.9%) agreed with the expected substitution ratio (12.5%), and a minimum set of 19 RCSLs represented the entire H602 genome. Phenotypes of five qualitative and nine quantitative traits were scored in both the RCSLs and DHLs. Five qualitative traits were localized as morphological markers on the linkage map of the DHLs, and these molecular markers were aligned on the respective chromosomal regions in the RCSLs. Simple and composite interval mapping procedures detected a total of 18 and 24 QTLs for nine qualitative traits on the RCSLs and DHLs, respectively. Several QTLs were localized at coincident or very close regions on both linkage maps. In spite of general inferior agronomic performances in wild barley, several H602 QTL alleles showed agronomically positive effects. These RCSLs should contribute to substitution of favorable alleles from wild barley into cultivated barley. These RCSLs are also available as sources of near isogenic lines, with which we can apply advanced genetic analysis methods such as isolation of QTLs and detection of epistatic interactions among QTLs.
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differential al resistance and citrate secretion in barley Hordeum Vulgare l
Planta, 2003Co-Authors: Kazuhiro Sato, Zhuqing Zhao, Jian Feng, Kazuyoshi TakedaAbstract:While barley (Hordeum Vulgare L.) is the most sensitive species to Al toxicity among small-grain crops, variation in Al resistance between cultivars does exist. We examined the mechanism responsible for differential Al resistance in 21 barley varieties. Citrate was secreted from the roots in response to Al stress. A positive correlation between citrate secretion and Al resistance [(root elongation with Al)/(root elongation without Al)] and a negative correlation between citrate secretion and Al content of root apices, were obtained, suggesting that citrate secretion from the root apices plays an important role in excluding Al and thereby detoxifying Al. The Al-induced secretion of citrate was characterized using an Al-resistant variety (Sigurdkorn) and an Al-sensitive variety (Kearney). In Sigurdkorn, Al-induced secretion of citrate occurred within 20 min, and the secretion did not increase with increasing external Al concentration. The Al-induced citrate secretion ceased at low temperature (6 °C) and was inhibited by anion-channel inhibitors. Internal citrate content of root apices was increased by Al exposure in Sigurdkorn, but was not affected in Kearney. The activity of citrate synthase was unaffected by Al in both Al-resistant and Al-sensitive varieties. The secretion rate of organic acid anions from barley was the lowest among wheat, rye and triticale.
Kiyosumi Hori - One of the best experts on this subject based on the ideXlab platform.
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qtl analysis in recombinant chromosome substitution lines and doubled haploid lines derived from a cross between Hordeum Vulgare ssp Vulgare and Hordeum Vulgare ssp spontaneum
Molecular Breeding, 2005Co-Authors: Kiyosumi Hori, Kazuhiro Sato, Nami Nankaku, Kazuyoshi TakedaAbstract:Recombinant chromosome substitution lines (RCSLs) were developed in BC3 generation to introduce segments of a wild barley strain ‘H602’ (Hordeum Vulgare ssp. spontaneum) into a barley cultivar ‘Haruna Nijo’ (H. Vulgare ssp. Vulgare) genetic background. One hundred thirty four RCSLs were genotyped by 25 SSR and 60 EST markers, which were localized on a linkage map of doubled haploid lines (DHLs) derived from the same cross combination. Graphical genotyping revealed that the observed average substitution ratio of H602 segment (12.9%) agreed with the expected substitution ratio (12.5%), and a minimum set of 19 RCSLs represented the entire H602 genome. Phenotypes of five qualitative and nine quantitative traits were scored in both the RCSLs and DHLs. Five qualitative traits were localized as morphological markers on the linkage map of the DHLs, and these molecular markers were aligned on the respective chromosomal regions in the RCSLs. Simple and composite interval mapping procedures detected a total of 18 and 24 QTLs for nine qualitative traits on the RCSLs and DHLs, respectively. Several QTLs were localized at coincident or very close regions on both linkage maps. In spite of general inferior agronomic performances in wild barley, several H602 QTL alleles showed agronomically positive effects. These RCSLs should contribute to substitution of favorable alleles from wild barley into cultivated barley. These RCSLs are also available as sources of near isogenic lines, with which we can apply advanced genetic analysis methods such as isolation of QTLs and detection of epistatic interactions among QTLs.
Nicholas C Collins - One of the best experts on this subject based on the ideXlab platform.
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hvnax3 a locus controlling shoot sodium exclusion derived from wild barley Hordeum Vulgare ssp spontaneum
Functional & Integrative Genomics, 2010Co-Authors: Yuri Shavrukov, Mark Tester, Narendra K Gupta, Junji Miyazaki, Manahil N Baho, K J Chalmers, Peter Langridge, Nicholas C CollinsAbstract:Previous work identified the wild barley (Hordeum Vulgare ssp. spontaneum) accession CPI-71284-48 as being capable of limiting sodium (Na(+)) accumulation in the shoots under saline hydroponic growth conditions. Quantitative trait locus (QTL) analysis using a cross between CPI-71284-48 and a selection of the cultivated barley (H. Vulgare ssp. Vulgare) cultivar Barque (Barque-73, a moderate Na(+) excluder) attributed the control of the Na(+) exclusion trait from CPI-71284-48 to a single locus on the short arm of chromosome 7H, which was named HvNax3. The locus reduced shoot Na(+) accumulation by 10-25% in plants grown in 150 mM NaCl. Markers generated using colinearity with rice and Brachypodium, together with the analysis of introgression lines and F(2) and F(3) families, enabled HvNax3 to be mapped to a 1.3-cM interval. Genes from the corresponding rice and Brachypodium intervals encode 16 different classes of proteins and include several plausible candidates for HvNax3. The potential of HvNax3 to provide a useful trait contributing to salinity tolerance in cultivated barley is discussed.
Peter Langridge - One of the best experts on this subject based on the ideXlab platform.
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hvzip7 mediates zinc accumulation in barley Hordeum Vulgare at moderately high zinc supply
New Phytologist, 2014Co-Authors: Jingwen Tiong, Peter Langridge, G K Mcdonald, Yusuf Genc, Pai Pedas, Julie Hayes, John Toubia, Chun Y HuangAbstract:Summary High expression of zinc (Zn)-regulated, iron-regulated transporter-like protein (ZIP) genes increases root Zn uptake in dicots, leading to high accumulation of Zn in shoots. However, none of the ZIP genes tested previously in monocots could enhance shoot Zn accumulation. In this report, barley (Hordeum Vulgare) HvZIP7 was investigated for its functions in Zn transport. The functions of HvZIP7 in planta were studied using in situ hybridization and transient analysis of subcellular localization with a green fluorescent protein (GFP) reporter. Transgenic barley lines overexpressing HvZIP7 were also generated to further understand the functions of HvZIP7 in metal transport. HvZIP7 is strongly induced by Zn deficiency, primarily in vascular tissues of roots and leaves, and its protein was localized in the plasma membrane. These properties are similar to its closely related homologs in dicots. Overexpression of HvZIP7 in barley plants increased Zn uptake when moderately high concentrations of Zn were supplied. Significantly, there was a specific enhancement of shoot Zn accumulation, with no measurable increase in iron (Fe), manganese (Mn), copper (Cu) or cadmium (Cd). HvZIP7 displays characteristics of low-affinity Zn transport. The unique function of HvZIP7 provides new insights into the role of ZIP genes in Zn homeostasis in monocots, and offers opportunities to develop Zn biofortification strategies in cereals.
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hvnax3 a locus controlling shoot sodium exclusion derived from wild barley Hordeum Vulgare ssp spontaneum
Functional & Integrative Genomics, 2010Co-Authors: Yuri Shavrukov, Mark Tester, Narendra K Gupta, Junji Miyazaki, Manahil N Baho, K J Chalmers, Peter Langridge, Nicholas C CollinsAbstract:Previous work identified the wild barley (Hordeum Vulgare ssp. spontaneum) accession CPI-71284-48 as being capable of limiting sodium (Na(+)) accumulation in the shoots under saline hydroponic growth conditions. Quantitative trait locus (QTL) analysis using a cross between CPI-71284-48 and a selection of the cultivated barley (H. Vulgare ssp. Vulgare) cultivar Barque (Barque-73, a moderate Na(+) excluder) attributed the control of the Na(+) exclusion trait from CPI-71284-48 to a single locus on the short arm of chromosome 7H, which was named HvNax3. The locus reduced shoot Na(+) accumulation by 10-25% in plants grown in 150 mM NaCl. Markers generated using colinearity with rice and Brachypodium, together with the analysis of introgression lines and F(2) and F(3) families, enabled HvNax3 to be mapped to a 1.3-cM interval. Genes from the corresponding rice and Brachypodium intervals encode 16 different classes of proteins and include several plausible candidates for HvNax3. The potential of HvNax3 to provide a useful trait contributing to salinity tolerance in cultivated barley is discussed.
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extreme population dependent linkage disequilibrium detected in an inbreeding plant species Hordeum Vulgare
Genetics, 2006Co-Authors: Katherine S Caldwell, Joanne Russell, Peter Langridge, W PowellAbstract:In human genetics a detailed knowledge of linkage disequilibrium (LD) is considered a prerequisite for effective population-based, high-resolution gene mapping and cloning. Similar opportunities exist for plants; however, differences in breeding system and population history need to be considered. Here we report a detailed study of localized LD in different populations of an inbreeding crop species. We measured LD between and within four gene loci within the region surrounding the hardness locus in three different gene pools of barley (Hordeum Vulgare). We demonstrate that LD extends to at least 212 kb in elite barley cultivars but is rapidly eroded in related inbreeding ancestral populations. Our results indicate that haplotype-based sequence analysis in multiple populations will provide new opportunities to adjust the resolution of association studies in inbreeding crop species.