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Molecular Characterization and SNP Markers of the β-purothionin Gene in Einkorn Wheats

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Agricultural Sciences in China 2009年第9期8卷 1019-1027页

作者： LI Jing-qiong zheng you-liang WEI Yu-ming Triticeae Research Institute Sichuan Agricultural University Ya ＂an 625014 P.R. China Key Laboratory of Crop Genetic Resources and Improvement in Southwest China Ministry of Education/Sichuan Agricultural University Ya＇an 625014 P.R.China

Forty-three gene sequences encoding purothionin were characterized from the three species or subspecies of einkorn wheats. These sequences contained 887 bp, among which 92 SNPs including 29 indel loci were detected, giving an average SNP frequency of one SNP per 9.64 bases. According to these sequences, 5 SNP markers were successfully designed, which were used to mine the variations ofpurothionin genes of 102 einkorn wheat accessions. Based on the 5 detected SNP loci, 102 einkorn wheat accessions could be divided into 21 haplotypes, among which 11 haplotypes contained a single sample. Phylogenetic analysis indicated that the purothionin genes from einkorn wheats were more closely related to those from D genome than B genome. Seven out of the 43 gene sequences were assumed to be pseudogenes by the definition of containing in-frame stop codons and small insertions/deletions leading to frameshift. In the remaining 36 amino acid sequences, the 8 Cys and Tyr-13 loci in the mature thionin domain which played important roles in the biological activities were all conserved, whereas there were some varieties occurred in some other important amino acid residues such as Lys and Arg.

关键词： einkorn wheats purothionin SNP haplotype

Analysis of LMW-GS,α-and γ-Gliadin Gene Coding Sequences from Triticum macha

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Agricultural Sciences in China 2010年第2期9卷 163-169页

作者： XIONG Li-juan WANG Ji-rui zheng you-liang Triticeae Research Institute Sichuan Agricultural University Ya＇an 625014 P.R.China Key Laboratory of Southwestern Crop Germplasm Utilization Ministry of Agriculture Ya＇an 625014 P.R.China

Novel LMW-GS （low molecular weight glutenin subunit）,α- and γ-gliadin from Triticum macha accessions were characterized via genomic PCR, which can do favor to improve the wheat quality. The complete coding regions of two α-gliadin, two γ-gliadin and two LMW-GS gene sequences, which designed as Gli-Mal, Gli-Ma2, Gli-Mrl, Gli-Mr2, Glu-LM1 and Glu-LM2, encoded the mature proteins with 307, 241, 348, 302, 474 and 377 amino acid residues, respectively. Gli-Mal and Gli-Ma2 were recognized as pseudogenes due to the in-frame stop codons. The amino acid sequences deduced from these gene sequences were characterized with the typical structure of α- or γ-gliadin or LMW- m type proteins with the exception of Gli-Ma2. Phylogenetic analysis showed Gli-Mal was closely related to those from T. aestivum, whereas Gli-Ma2 seemed to be more homologous with the gene sequences from Dasypyrum breviaristatum. Gli-Mrl was closely related to those from T. turgidum ssp. dicoccoides, while Gli-Mr2 was the nearest to those from T. aestivum. Glu-LM1 was closely related to those from Aegilops tauschii, whereas GIu-LM2 seemed to be more homologous with those from T. durum.

关键词： T. macha α-gliadin γ-gliadin LMW-GS gene clone sequence analysis

SNP Analysis and Haplotype Identification in Chymotrypsin Inhibitor-2 (CI-2) Gene of Barley

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Agricultural Sciences in China 2009年第1期8卷 8-14页

作者： ZENG Xiang-hui WEI Yu-ming JIANG Qian-tao QI Peng-fei zheng you-liang Triticeae Research Institute Sichuan Agricultural University Ya＇an 625014 P.R.China Key Laboratory of Crop Genetic Resources and Improvement in Southwest China Ministry of Education/Sichuan Agricultural University Ya＇an 625014 P.R.China

Barley chymotrypsin inhibitor-2 （CI-2） was considered to be a promising candidate for enhancing the nutritional value of other cereals by increasing its concentration as it is rich in lysine than any other storage protein. Also, it was proposed that CI-2 might play an important role in the inhibition of proteolytic enzymes from pests or pathogens as CI-2 can strongly inhibit chymotrypsin and subtilisin. In this study, a total of 93 CI-2 gene sequences were isolated from wild and cultivated barley. 48 SNPs and 4 indels were detected across the entire sequences. The frequency of SNPs in the noncoding region （1 out of 9 bases） was slightly higher than that in the coding region （1 out of 10.7 bases）. In all, 33.3% of the candidate cSNPs resulted in amino acid changes. As a total, the 24 cSNPs resulted in 15 amino acid changes. Ten distinguishable haplotypes were detected, among which 3 haplotypes were shared in the most barley accessions, whereas the rest of the haplotypes appeared at a lower frequency. In addition, three haplotypes （haplotype 4, 8, and 9） were unique for single accessions. These results suggested that low diversity at the CI-2 locus was detected among the cultivated and wild barley.

关键词： barley chymotrypsin inhibitor SNP haplotype

Comparative Analysis of Six Triticum turgidum L. Subspecies for Acid and Aluminum Tolerance

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Agricultural Sciences in China 2010年第5期9卷 642-650页

作者： DAI Shou-fen YAN Ze-hong LIU Deng-cai WEI Yu-ming zheng you-liang Triticeae Research Institute Sichuan Agricultural University Chengdu 611130 P.R.China

The aluminum （A1） tolerance of hexaploid wheat and rye has been extensively studied. However, the A1 tolerance of tetraploid wheat （Triticum turgidum L.）, the AABB genome donor of hexaploid wheat, has not been well characterized. To understand the A1 tolerance of tetraploid wheat and identify potentially new sources of tolerance to acidic soils, 254 Triticum turgidum wheat lines, including six subspecies of T. turdigum ssp. dieoccoides, ssp. dicoccon, ssp. carthlicum, ssp. turgidum, ssp. durum, and ssp. polinicum, were screened for acid and A1 tolerance by measuring the root regenerate lengths and the tolerance indices in acid nutrient culture solution containing A1. Significant differences were observed either among or within tetraploid wheat subspecies on the RRL （root regenerate lengths）. The orders for average RRL among subspecies in pH 7.00, pH 4.50 and pH 4.50 ＋ 50μmol L^-1 A1^3＋ were carthlicum ≥ turgidum ≥ durum ≥ dicoccoides polinicum ≥ dicoccon, carthlicum ≥ turgidum ≥ durum ≥ polinicum ≥ dicoccon ≥ dicoccoides and durum ≥ dicoccoides carthlicum ≥ turgidum ≥polinicum ≥ dicoccon, respectively. Significant difference was also observed on the root acid tolerance index （RT11） and root A1 tolerance index （RTI2） either among or within tetraploid wheat subspecies. Compared to RTI2, RTI1 varied in a wide range but with large value. The orders of the average RTI1 and RTI2 among subspecies were polinicum ≥ dicoccon ≥ carthlicum ≥ dicoccoides ≥ turgidum ≥durum, and dicoccoides ≥ durum ≥ turgidum ≥polinicum carthlicum ≥dicoccon, respectively. Significant difference on acid and A1 tolerance was existed either among or within subspecies. Some potentially tolerance germplasms different from those derived from hexaploid wheat, including 42 acid tolerance and 41 A1 tolerance lines, were identified in 254 tetraploid wheat lines. They provide new sources for hexaploid wheat acid and A1 tolerance improvement.

关键词： Triticum turgidum A1 tolerance acid tolerance

Sequence Polymorphisms and Phylogenetic Relationships of hina Gene in Wild Barley from Tibet, China

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Agricultural Sciences in China 2008年第7期7卷 796-803页

作者： YANG Shi-dong WEI Yu-ming QI Peng-fei zheng you-liang Triticeae Research Institute Sichuan Agricultural University Ya＇an 625014 P..R.China Key Laboratory of Crop Genetic Resources and Improvement in Southwest China Ministry of Education/Sichuan Agricultural University Ya＇an 625014 P.R. China

The hina gene encodes a HINA protein in seeds of barley （Hordeum vulgare）, which was known to affect the grain hardness. 171 hina gene sequences from Tibetan wild barley accessions and worldwide were characterized. Across 1 452 nucleotides of 171 hina genes, 152 SNPs were detected, giving an average frequency of one SNP per 9.5 bases. There were 93 singleton variable sites （the nucleotide polymorphism only observed in a single accession）, 59 polymorphic sites （the polymorphisms found in two or more accessions） and 8 indels. A total of 18 haplotypes were defined, and most of the barley accessions shared one gene haplotype. H. spontaneum had a wider haplotype distribution. Through the analysis of median-joining network of the 18 haplotypes, 4 haplotype groups were found, which were testified by neighbor-joining tree based on the complete sequence alignment. Extremely low level of hina gene diversity was observed in Tibetan wild barley accessions, indicating that Tibet is unlikely a center of origin for cultivated barley.

关键词： Tibetan wild barley hina SNP haplotype median-joining network

Variations of Single Nucleotide Polymorphism (SNP) of Hordoindoline a Gene (hina) and Its Relationships with Kernel Hardness in 92 North American Barley Varieties (Hordeum vulgare L.)

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Agricultural Sciences in China 2009年第12期8卷 1440-1447页

作者： CHEN Guo-yue YANG Shi-dong LI Wei-tao LI Wei WEI Yu-ming zheng you-liang Triticeae Research Institute Sichuan Agricultural University Ya'an 625014 P.R.China Key Laboratory of Crop Genetic Resources and Improvement in Southwest China Ministry of Education/Sichuan Agricultural University Ya'an 625014 P.R. China College of Agronomy Sichuan Agricultural University Ya'an 625014 P.R.China

Grain texture in barley （Hordeum vulgare L.） is an important quality character. The single nucleotide polymorphisms （SNPs） in Hordoindoline a （hina） gene and its relationship with hardness index among North American harley cultivars were investigated. The hina genes in 36 cultivars were sequenced for the SNP analyses, and 17 sets of SNP primers were designed to detect the SNP variations of hina locus in 92 North American barley cultivars. SNP detection indicated that there were four haplotypes in the hina genes of 92 barley cultivars, and haplotype 01 and 02 were shared by 68 and 14 cultivars, respectively, suggesting that there was a very limited diversity in hina genes among North American barley cultivars. Despite the wide range in hardness exists in 92 barley cultivars, however, unlike wheat, where a clear relationship has been demonstrated between a number of SNPs in the wheat hardness genes and quality （soft or hard wheat）, there was no such relationship for barley. The genotypes used in this study demonstrated that there was a low level of polymorphism in hina gene in North American barley cultivars and these polymorphisms had no impact on grain hardness.

关键词： barley Hordoindoline a gene hardness SNP haplotype

Genetic Variation in Triticum turgidum L. ssp. turgidum Landraces from China Assessed by EST-SSR Markers

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Agricultural Sciences in China 2008年第9期7卷 1029-1036页

作者： LI Wei DONG Pan WEI Yu-ming CHENG Guo-yue zheng you-liang Key Laboratory of Crop Genetic Resources and Improvement in Southwest China Ministry of Education/Sichuan Agricultural University Ya＇an 625014 P.R.China Triticeae Research Institute Sichuan Agricultural University Dujiangyan 611830 P.R.China College of Agronomy Sichuan Agricultural University Ya＇an 625014 P.R.China

It was helpful for the wheat improvement to evaluate the genetic resources of Triticum turgidum L. ssp. turgidum landraces. In this study, 68 turgidum landraces accessions, belonging to four geographic populations in China, were investigated by using EST-SSR markers. A total of 63 alleles were detected on 22 EST-SSR loci, and the number of alleles on each locus ranged from 1 to 5, with an average of 2.9. The results of the analysis of molecular variance （AMOVA） indicated that 92.5% of the total variations was attributed to the genetic variations within population, whereas only 7.5% variations among populations. Although the four populations had similar genetic diversity parameters, Sichuan population was yet distinguished from other populations when comparing the population samples in pairs. Significant correlations were detected by the statistic analysis among six genetic diversity parameters among each other. The selection difference between heterozygosty and homozygosty was also observed among different EST-SSR locus. The genetic similarity （GS） ranged from 0.18 to 0.98, with the mean of 0.72, and all accessions could be clustered into 7 groups. The dendrogram suggested that the genetic relationships among turgidum accessions evaluated by EST-SSR markers were unrelated to their geographic distributions. These results implied that turgidum landraces from China had the unique characters of genetic diversity.

关键词： T. turgidum L. ssp. turgidum EST-SSR markers genetic variation genetic structure

Evaluation on Chinese Bread Wheat Landraces for Low pH and Aluminum Tolerance Using Hydroponic Screening

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Agricultural Sciences in China 2009年第3期8卷 285-292页

作者： DAI Shou-fen YAN Ze-hong LIU Deng-cai ZHANG Lian-quan WEI Yu-ming zheng you-liang Triticeae Research Institute Sichuan Agricultural University Dujiangyan 611830 P.R.China

Aluminum （Al） toxicity often takes place in acidic soils with a pH of 5.5 or lower. Breeding and cultivation of Al tolerance wheat can partially protect wheat escaping from Al toxicity. The scarcity of the tolerant sources impedes the wheat breeding. In order to find new Al tolerance sources, we screened 173 bread wheat landraces from Tibet of China using hydroponic screening. It was indicated that：（1） There were diversities on the root regenerate length （RRL）. The RRL of a large of landraces were longer than 7.00 cm in pH 7 （58.38%） and pH 4.5 （66.47%）, but shorter than 5.00 cm in pH 4.5 ＋50μM Al^3＋（80.93%）. The low pH showed either promotion or restraining effects depend on landraces, but Al toxicity under low pH only showed restraining effects on the root elongation. （2） There were also diversities on root tolerance index of low pH （RTI 1） or root aluminum tolerance index （RTI2） among cultivars. The RTI1 varied from a narrow range but with relatively high value （0.8722-1.2953） in comparison with that of RTI2 （0.3829-1.0058）, and the RTI1 of approximately 60% landraces was higher than 1.0000, the RTI2 of only 19.07% landraces was higher than 0.7000, suggesting that Al toxicity acted as an important factor for the reduction of the root elongation under acidic soils. （3） The RTI 1 of many wheats was higher than 1.0000, and As2256 and As2295 were the most tolerant for low pH, with RTI1 1.2953 and 1.2925, respectively. （4） Based on RTI2, seven wheats showed similar or higher tolerance to Al toxicity than Chinese Spring （CS）, a known tolerance wheat. Much better tolerance existed in landraces of As1543 and As1242, which can be used as the new parents for Al tolerant breeding.

关键词： bread wheat root regenerate length tolerance index aluminum tolerance hydroponic screening

Molecular mapping of a stripe rust resistance gene in Chinese wheat cultivar Mianmai 41

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Journal of Integrative Agriculture 2015年第2期14卷 295-304页

作者： REN Yong LI Sheng-rong WEI Yu-ming ZHOU Qiang DU Xiao-ying HE Yuan-jiang zheng you-liang Triticeae Research Institute Sichuan Agricultural University Mianyang Institute of Agricultural Science/Mianyang Wheat Experimental Station China Agriculture Research System(CARS)

Stripe rust, caused by Puccinia striiformis f. sp. tritici（Pst）, is one of the most damaging diseases of wheat. Chinese wheat cultivar Mianmai 41 showed high resistance against most of the prevailing Pst races in China. Genetic analysis of the F1, F2 and F2：3 populations from a cross between Mianmai 41 and a susceptible line Mingxian 169 indicated that resistance to Pst race CYR32 was conferred by a single dominant gene, temporarily designated as Yr MY41. Molecular marker analysis placed the gene on chromosome 1B near the centromere. Six co-dominant genomic SSR markers Xwmc329, Xwmc406, Xgwm18, Xgwm131, Xgwm413, and Xbarc312, and one STS marker Xwe173 linked with the resistance gene. The two closest flanking SSR markers were Xgwm18 and Xwmc406, with genetic distances of 2.0 and 4.9 c M, respectively. A seedling test with 29 Pst isolates indicated the reaction patterns of Mianmai 41 were different from those of lines carrying Yr3, Yr9, Yr10, Yr15, Yr26, and Yr CH42 on chromosome 1B. Allelic tests indicated that Yr MY41 is likely a new allele at Yr26 locus.

关键词： Triticum aestivum L. yellow rust simple sequence repeat(SSR) marker sequence tagged site(STS) marker