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Zongyu Zhang - One of the best experts on this subject based on the ideXlab platform.

  • elymus nutans genes for seed shattering and candidate gene derived est ssr markers for Germplasm Evaluation
    BMC Plant Biology, 2019
    Co-Authors: Yongqiang Zhao, Junchao Zhang, Zongyu Zhang
    Abstract:

    Elymus nutans and E. sibiricus are two important forage grasses of the genus Elymus. But they are difficult to grow for commercial seed production due to serious seed shattering. We conducted a comparative transcriptome analysis of abscission zone to find possible transcription changes associated with seed shattering, explore candidate genes involved in seed shattering and identify candidate gene-based EST-SSR markers for Germplasm Evaluation. cDNA libraries from abscission zone (AZ) and non-abscission zone (NAZ) tissues of E. nutans were constructed and sequenced. A total of 111,667 unigenes were annotated and 7644 differentially expressed transcripts (DETs) were predicted, corresponding to 6936 up-regulated in AZ and 708 down-regulated in NAZ. We identified 489 candidate genes related to transcription factor, cell wall hydrolysis or modification, hydrolase activity, phytohormone signaling and response, lignin biosynthesis, and signal transduction or protein turnover. Eleven similar candidate genes involved in polygalacturonase activity, hydrolase activity, and mitogen-activated protein kinase were up-regulated in the abscission zone of the two Elymus species, suggesting these genes may have specific function for abscission zone development and seed shattering. A total of 67 polymorphic EST-SSR markers were developed and characterized based on the sequences of these candidate genes. Fourteen polymorphic EST-SSR primers were finally used to study genetic diversity in 48 E. nutans genotypes with contrasting seed shattering habit. The dendrogram based on molecular data showed that most accessions with similar seed shattering degree tended to group together. The expression data generated from this study provides an important resource for future molecular biological research. Many DETs were associated with abscission zone development, and EST-SSR loci related to candidate genes may have potential application in identifying trait-associated markers in E. nutans in the future.

  • Additional file 3: of Elymus nutans genes for seed shattering and candidate gene-derived EST-SSR markers for Germplasm Evaluation
    2019
    Co-Authors: Yongqiang Zhao, Junchao Zhang, Zongyu Zhang, Wengang Xie
    Abstract:

    Table S2. Differentially expressed transcripts related to seed shattering found in abscission zone and non-abscission zone. (XLS 357 kb

  • Elymus nutans genes for seed shattering and candidate gene-derived EST-SSR markers for Germplasm Evaluation
    BMC, 2019
    Co-Authors: Yongqiang Zhao, Junchao Zhang, Zongyu Zhang, Wengang Xie
    Abstract:

    Abstract Background Elymus nutans and E. sibiricus are two important forage grasses of the genus Elymus. But they are difficult to grow for commercial seed production due to serious seed shattering. We conducted a comparative transcriptome analysis of abscission zone to find possible transcription changes associated with seed shattering, explore candidate genes involved in seed shattering and identify candidate gene-based EST-SSR markers for Germplasm Evaluation. Results cDNA libraries from abscission zone (AZ) and non-abscission zone (NAZ) tissues of E. nutans were constructed and sequenced. A total of 111,667 unigenes were annotated and 7644 differentially expressed transcripts (DETs) were predicted, corresponding to 6936 up-regulated in AZ and 708 down-regulated in NAZ. We identified 489 candidate genes related to transcription factor, cell wall hydrolysis or modification, hydrolase activity, phytohormone signaling and response, lignin biosynthesis, and signal transduction or protein turnover. Eleven similar candidate genes involved in polygalacturonase activity, hydrolase activity, and mitogen-activated protein kinase were up-regulated in the abscission zone of the two Elymus species, suggesting these genes may have specific function for abscission zone development and seed shattering. A total of 67 polymorphic EST-SSR markers were developed and characterized based on the sequences of these candidate genes. Fourteen polymorphic EST-SSR primers were finally used to study genetic diversity in 48 E. nutans genotypes with contrasting seed shattering habit. The dendrogram based on molecular data showed that most accessions with similar seed shattering degree tended to group together. Conclusions The expression data generated from this study provides an important resource for future molecular biological research. Many DETs were associated with abscission zone development, and EST-SSR loci related to candidate genes may have potential application in identifying trait-associated markers in E. nutans in the future

  • Additional file 4: of Elymus nutans genes for seed shattering and candidate gene-derived EST-SSR markers for Germplasm Evaluation
    2019
    Co-Authors: Yongqiang Zhao, Junchao Zhang, Zongyu Zhang, Wengang Xie
    Abstract:

    Table S3. Differentially expressed transcripts related to seed shattering found in abscission zone at 21 days (AZ-21) and 28 days (AZ-28) after heading. (XLS 165 kb

Yongqiang Zhao - One of the best experts on this subject based on the ideXlab platform.

  • elymus nutans genes for seed shattering and candidate gene derived est ssr markers for Germplasm Evaluation
    BMC Plant Biology, 2019
    Co-Authors: Yongqiang Zhao, Junchao Zhang, Zongyu Zhang
    Abstract:

    Elymus nutans and E. sibiricus are two important forage grasses of the genus Elymus. But they are difficult to grow for commercial seed production due to serious seed shattering. We conducted a comparative transcriptome analysis of abscission zone to find possible transcription changes associated with seed shattering, explore candidate genes involved in seed shattering and identify candidate gene-based EST-SSR markers for Germplasm Evaluation. cDNA libraries from abscission zone (AZ) and non-abscission zone (NAZ) tissues of E. nutans were constructed and sequenced. A total of 111,667 unigenes were annotated and 7644 differentially expressed transcripts (DETs) were predicted, corresponding to 6936 up-regulated in AZ and 708 down-regulated in NAZ. We identified 489 candidate genes related to transcription factor, cell wall hydrolysis or modification, hydrolase activity, phytohormone signaling and response, lignin biosynthesis, and signal transduction or protein turnover. Eleven similar candidate genes involved in polygalacturonase activity, hydrolase activity, and mitogen-activated protein kinase were up-regulated in the abscission zone of the two Elymus species, suggesting these genes may have specific function for abscission zone development and seed shattering. A total of 67 polymorphic EST-SSR markers were developed and characterized based on the sequences of these candidate genes. Fourteen polymorphic EST-SSR primers were finally used to study genetic diversity in 48 E. nutans genotypes with contrasting seed shattering habit. The dendrogram based on molecular data showed that most accessions with similar seed shattering degree tended to group together. The expression data generated from this study provides an important resource for future molecular biological research. Many DETs were associated with abscission zone development, and EST-SSR loci related to candidate genes may have potential application in identifying trait-associated markers in E. nutans in the future.

  • Additional file 3: of Elymus nutans genes for seed shattering and candidate gene-derived EST-SSR markers for Germplasm Evaluation
    2019
    Co-Authors: Yongqiang Zhao, Junchao Zhang, Zongyu Zhang, Wengang Xie
    Abstract:

    Table S2. Differentially expressed transcripts related to seed shattering found in abscission zone and non-abscission zone. (XLS 357 kb

  • Elymus nutans genes for seed shattering and candidate gene-derived EST-SSR markers for Germplasm Evaluation
    BMC, 2019
    Co-Authors: Yongqiang Zhao, Junchao Zhang, Zongyu Zhang, Wengang Xie
    Abstract:

    Abstract Background Elymus nutans and E. sibiricus are two important forage grasses of the genus Elymus. But they are difficult to grow for commercial seed production due to serious seed shattering. We conducted a comparative transcriptome analysis of abscission zone to find possible transcription changes associated with seed shattering, explore candidate genes involved in seed shattering and identify candidate gene-based EST-SSR markers for Germplasm Evaluation. Results cDNA libraries from abscission zone (AZ) and non-abscission zone (NAZ) tissues of E. nutans were constructed and sequenced. A total of 111,667 unigenes were annotated and 7644 differentially expressed transcripts (DETs) were predicted, corresponding to 6936 up-regulated in AZ and 708 down-regulated in NAZ. We identified 489 candidate genes related to transcription factor, cell wall hydrolysis or modification, hydrolase activity, phytohormone signaling and response, lignin biosynthesis, and signal transduction or protein turnover. Eleven similar candidate genes involved in polygalacturonase activity, hydrolase activity, and mitogen-activated protein kinase were up-regulated in the abscission zone of the two Elymus species, suggesting these genes may have specific function for abscission zone development and seed shattering. A total of 67 polymorphic EST-SSR markers were developed and characterized based on the sequences of these candidate genes. Fourteen polymorphic EST-SSR primers were finally used to study genetic diversity in 48 E. nutans genotypes with contrasting seed shattering habit. The dendrogram based on molecular data showed that most accessions with similar seed shattering degree tended to group together. Conclusions The expression data generated from this study provides an important resource for future molecular biological research. Many DETs were associated with abscission zone development, and EST-SSR loci related to candidate genes may have potential application in identifying trait-associated markers in E. nutans in the future

  • Additional file 4: of Elymus nutans genes for seed shattering and candidate gene-derived EST-SSR markers for Germplasm Evaluation
    2019
    Co-Authors: Yongqiang Zhao, Junchao Zhang, Zongyu Zhang, Wengang Xie
    Abstract:

    Table S3. Differentially expressed transcripts related to seed shattering found in abscission zone at 21 days (AZ-21) and 28 days (AZ-28) after heading. (XLS 165 kb

Junchao Zhang - One of the best experts on this subject based on the ideXlab platform.

  • elymus nutans genes for seed shattering and candidate gene derived est ssr markers for Germplasm Evaluation
    BMC Plant Biology, 2019
    Co-Authors: Yongqiang Zhao, Junchao Zhang, Zongyu Zhang
    Abstract:

    Elymus nutans and E. sibiricus are two important forage grasses of the genus Elymus. But they are difficult to grow for commercial seed production due to serious seed shattering. We conducted a comparative transcriptome analysis of abscission zone to find possible transcription changes associated with seed shattering, explore candidate genes involved in seed shattering and identify candidate gene-based EST-SSR markers for Germplasm Evaluation. cDNA libraries from abscission zone (AZ) and non-abscission zone (NAZ) tissues of E. nutans were constructed and sequenced. A total of 111,667 unigenes were annotated and 7644 differentially expressed transcripts (DETs) were predicted, corresponding to 6936 up-regulated in AZ and 708 down-regulated in NAZ. We identified 489 candidate genes related to transcription factor, cell wall hydrolysis or modification, hydrolase activity, phytohormone signaling and response, lignin biosynthesis, and signal transduction or protein turnover. Eleven similar candidate genes involved in polygalacturonase activity, hydrolase activity, and mitogen-activated protein kinase were up-regulated in the abscission zone of the two Elymus species, suggesting these genes may have specific function for abscission zone development and seed shattering. A total of 67 polymorphic EST-SSR markers were developed and characterized based on the sequences of these candidate genes. Fourteen polymorphic EST-SSR primers were finally used to study genetic diversity in 48 E. nutans genotypes with contrasting seed shattering habit. The dendrogram based on molecular data showed that most accessions with similar seed shattering degree tended to group together. The expression data generated from this study provides an important resource for future molecular biological research. Many DETs were associated with abscission zone development, and EST-SSR loci related to candidate genes may have potential application in identifying trait-associated markers in E. nutans in the future.

  • Additional file 3: of Elymus nutans genes for seed shattering and candidate gene-derived EST-SSR markers for Germplasm Evaluation
    2019
    Co-Authors: Yongqiang Zhao, Junchao Zhang, Zongyu Zhang, Wengang Xie
    Abstract:

    Table S2. Differentially expressed transcripts related to seed shattering found in abscission zone and non-abscission zone. (XLS 357 kb

  • Elymus nutans genes for seed shattering and candidate gene-derived EST-SSR markers for Germplasm Evaluation
    BMC, 2019
    Co-Authors: Yongqiang Zhao, Junchao Zhang, Zongyu Zhang, Wengang Xie
    Abstract:

    Abstract Background Elymus nutans and E. sibiricus are two important forage grasses of the genus Elymus. But they are difficult to grow for commercial seed production due to serious seed shattering. We conducted a comparative transcriptome analysis of abscission zone to find possible transcription changes associated with seed shattering, explore candidate genes involved in seed shattering and identify candidate gene-based EST-SSR markers for Germplasm Evaluation. Results cDNA libraries from abscission zone (AZ) and non-abscission zone (NAZ) tissues of E. nutans were constructed and sequenced. A total of 111,667 unigenes were annotated and 7644 differentially expressed transcripts (DETs) were predicted, corresponding to 6936 up-regulated in AZ and 708 down-regulated in NAZ. We identified 489 candidate genes related to transcription factor, cell wall hydrolysis or modification, hydrolase activity, phytohormone signaling and response, lignin biosynthesis, and signal transduction or protein turnover. Eleven similar candidate genes involved in polygalacturonase activity, hydrolase activity, and mitogen-activated protein kinase were up-regulated in the abscission zone of the two Elymus species, suggesting these genes may have specific function for abscission zone development and seed shattering. A total of 67 polymorphic EST-SSR markers were developed and characterized based on the sequences of these candidate genes. Fourteen polymorphic EST-SSR primers were finally used to study genetic diversity in 48 E. nutans genotypes with contrasting seed shattering habit. The dendrogram based on molecular data showed that most accessions with similar seed shattering degree tended to group together. Conclusions The expression data generated from this study provides an important resource for future molecular biological research. Many DETs were associated with abscission zone development, and EST-SSR loci related to candidate genes may have potential application in identifying trait-associated markers in E. nutans in the future

  • Additional file 4: of Elymus nutans genes for seed shattering and candidate gene-derived EST-SSR markers for Germplasm Evaluation
    2019
    Co-Authors: Yongqiang Zhao, Junchao Zhang, Zongyu Zhang, Wengang Xie
    Abstract:

    Table S3. Differentially expressed transcripts related to seed shattering found in abscission zone at 21 days (AZ-21) and 28 days (AZ-28) after heading. (XLS 165 kb

L D Van Vleck - One of the best experts on this subject based on the ideXlab platform.

  • comparisons of angus charolais galloway hereford longhorn nellore piedmontese salers and shorthorn breeds for weight weight adjusted for condition score height and condition score of cows
    Journal of Animal Science, 2004
    Co-Authors: J A Arango, Larry V. Cundiff, L D Van Vleck
    Abstract:

    Breed differences for weight (CW), height (CH), and condition score (CS) were estimated from records (n = 12,188) of 2- to 6-yr-old cows (n = 744) from Cycle IV of the U.S. Meat Animal Research Center's Germplasm Evaluation (GPE) Program. Cows were produced from mating Angus and Hereford dams to Angus, Hereford, Charolais, Shorthorn, Galloway, Longhorn, Nellore, Piedmontese, and Salers sires. Samples of Angus and Hereford sires were 1) reference sires born from 1962 through 1970 and 2) 1980s sires born in 1980 through 1987. The mixed model included cow age, season of measurement and their interactions, year of birth, pregnancy-lactation code (PL), and breed-group as fixed effects for CW and CS. Analyses of weight adjusted for condition score included CS as a linear covariate. The model for CH excluded PL. Random effects were additive genetic and permanent environmental effects associated with the cow. Differences among breed groups were significant (P < 0.05) for all traits and were maintained through maturity with few interchanges in ranking. The order of F 1 cows for weight was as follows: Charolais (506 to 635 kg for different ages), Shorthorn and Salers, reciprocal Hereford-Angus (HA) with 1980s sires, Nellore, HA with reference sires, Galloway, Piedmontese, and Longhorn (412 to 525 kg for different ages). Order for height was as follows: Nellore (136 to 140 cm), Charolais, Shorthorn, Salers, HA with 1980s sires, Piedmontese, Longhorn, Galloway and HA with reference sires (126 to 128 cm). Hereford and Angus cows with reference sires were generally lighter than those with 1980s sires. In general, breed differences for height followed those for weight except that F 1 Nellore cows were tallest, which may in part be due to Bos taurus-Bos indicus heterosis for size.

  • comparisons of angus braunvieh chianina hereford gelbvieh maine anjou and red poll sired cows for weight weight adjusted for body condition score height and body condition score
    Journal of Animal Science, 2002
    Co-Authors: J A Arango, Larry V. Cundiff, L D Van Vleck
    Abstract:

    Data from Angus, Hereford, and topcross cows (n = 641) from 2- to 8-yr-old daughters of seven breeds of sires included in Cycle II of the Germplasm Evaluation Program at the U.S. Meat Animal Research Center, comprising cow weight (CW, n = 15,698), height (CH, n = 15,676), and condition score (CS, n = 15,667), were used to estimate breed-group differences. Data were recorded in four seasons of each year (1975 to 1982). The mixed model included cow age, season of measurement, and their interactions, year of birth, pregnancy-lactation code (PL), and breed-group as fixed effects for CW and CS. Analyses of weight adjusted for condition score included CS as covariate. The model for CH excluded PL. Random effects were additive genetic and permanent environmental effects. Differences among breed-groups were significant for all traits at different ages and were maintained across ages, with few interchanges in ranking through maturity. Cows were ranked (by breed of sire) in the following order for weight: Red Poll (lightest), Hereford-Angus (reciprocal), Braunvieh, Gelbvieh, Maine Anjou, and Chianina (heaviest). In general, cows sired by breeds of British origin were lighter and shorter than those of continental origin. Differences in weight due to differences in condition seemed to be of small magnitude because making an adjustment for condition score did not affect rankings of breed groups across ages. Differences among breed groups for height were consistent with differences for weight. Cows from Chianina sires were taller than Hereford-Angus cows by 14 to 15 cm across ages. In this study, breed of sire effects were significantly different for the mature size of their daughters.

J A Arango - One of the best experts on this subject based on the ideXlab platform.

  • comparisons of angus charolais galloway hereford longhorn nellore piedmontese salers and shorthorn breeds for weight weight adjusted for condition score height and condition score of cows
    Journal of Animal Science, 2004
    Co-Authors: J A Arango, Larry V. Cundiff, L D Van Vleck
    Abstract:

    Breed differences for weight (CW), height (CH), and condition score (CS) were estimated from records (n = 12,188) of 2- to 6-yr-old cows (n = 744) from Cycle IV of the U.S. Meat Animal Research Center's Germplasm Evaluation (GPE) Program. Cows were produced from mating Angus and Hereford dams to Angus, Hereford, Charolais, Shorthorn, Galloway, Longhorn, Nellore, Piedmontese, and Salers sires. Samples of Angus and Hereford sires were 1) reference sires born from 1962 through 1970 and 2) 1980s sires born in 1980 through 1987. The mixed model included cow age, season of measurement and their interactions, year of birth, pregnancy-lactation code (PL), and breed-group as fixed effects for CW and CS. Analyses of weight adjusted for condition score included CS as a linear covariate. The model for CH excluded PL. Random effects were additive genetic and permanent environmental effects associated with the cow. Differences among breed groups were significant (P < 0.05) for all traits and were maintained through maturity with few interchanges in ranking. The order of F 1 cows for weight was as follows: Charolais (506 to 635 kg for different ages), Shorthorn and Salers, reciprocal Hereford-Angus (HA) with 1980s sires, Nellore, HA with reference sires, Galloway, Piedmontese, and Longhorn (412 to 525 kg for different ages). Order for height was as follows: Nellore (136 to 140 cm), Charolais, Shorthorn, Salers, HA with 1980s sires, Piedmontese, Longhorn, Galloway and HA with reference sires (126 to 128 cm). Hereford and Angus cows with reference sires were generally lighter than those with 1980s sires. In general, breed differences for height followed those for weight except that F 1 Nellore cows were tallest, which may in part be due to Bos taurus-Bos indicus heterosis for size.

  • comparisons of angus braunvieh chianina hereford gelbvieh maine anjou and red poll sired cows for weight weight adjusted for body condition score height and body condition score
    Journal of Animal Science, 2002
    Co-Authors: J A Arango, Larry V. Cundiff, L D Van Vleck
    Abstract:

    Data from Angus, Hereford, and topcross cows (n = 641) from 2- to 8-yr-old daughters of seven breeds of sires included in Cycle II of the Germplasm Evaluation Program at the U.S. Meat Animal Research Center, comprising cow weight (CW, n = 15,698), height (CH, n = 15,676), and condition score (CS, n = 15,667), were used to estimate breed-group differences. Data were recorded in four seasons of each year (1975 to 1982). The mixed model included cow age, season of measurement, and their interactions, year of birth, pregnancy-lactation code (PL), and breed-group as fixed effects for CW and CS. Analyses of weight adjusted for condition score included CS as covariate. The model for CH excluded PL. Random effects were additive genetic and permanent environmental effects. Differences among breed-groups were significant for all traits at different ages and were maintained across ages, with few interchanges in ranking through maturity. Cows were ranked (by breed of sire) in the following order for weight: Red Poll (lightest), Hereford-Angus (reciprocal), Braunvieh, Gelbvieh, Maine Anjou, and Chianina (heaviest). In general, cows sired by breeds of British origin were lighter and shorter than those of continental origin. Differences in weight due to differences in condition seemed to be of small magnitude because making an adjustment for condition score did not affect rankings of breed groups across ages. Differences among breed groups for height were consistent with differences for weight. Cows from Chianina sires were taller than Hereford-Angus cows by 14 to 15 cm across ages. In this study, breed of sire effects were significantly different for the mature size of their daughters.

  • breed comparisons of angus charolais hereford jersey limousin simmental and south devon for weight weight adjusted for body condition score height and body condition score of cows
    Journal of Animal Science, 2002
    Co-Authors: J A Arango, Larry V. Cundiff, L D Van Vleck
    Abstract:

    Breed means and differences for weight (CW, n = 19,851), height (CH, n = 14,553), and condition scores (CS, n = 19,536) recorded in four seasons per year were evaluated for 881 cows ranging from 2 to 7 yr of age from Cycle I of the Germplasm Evaluation Program at the U.S. Meat Animal Research Center. Cows were straightbred Herefords and Angus and top- crosses from mating of Hereford, Angus, South Devon, Jersey, Simmental, Limousin, and Charolais sires to Hereford and Angus dams. The model included cow age, season of measurement, and their interactions, with year of birth, pregnancy-lactation (PL) code, and breed group as fixed effects for CW and CS. Analyses of weight adjusted for condition score included CS as covariate. Model for CH excluded PL. Random effects were addi- tive genetic and permanent environmental effects. Data were analyzed by REML. Differences due to breeds of sire were significant for all traits. Differences were gen-

  • genetic parameters for weight weight adjusted for body condition score height and body condition score in beef cows
    Journal of Animal Science, 2002
    Co-Authors: J A Arango, Larry V. Cundiff, L D Van Vleck
    Abstract:

    Weight (CW, n = 61,798), weight ad- justed for condition score (WA), hip height (CH, n = 56,494), and condition score (CS, n = 61,434) of cows (2 through 8 yr of age) produced by crosses of 22 sire breeds with Angus and Hereford dams in the first four cycles of the Germplasm Evaluation (GPE) Program at the U.S. Meat Animal Research Center were used to estimate genetic parameters with REML. The model included sire breed, dam breed, age in years, season of measurement (1 to 4) and their interactions, and year of birth and pregnancy-lactation code (PL) as fixed ef- fects for CW and CS. The model for CH excluded PL. Random effects were additive genetic and permanent environmental effects. Univariate analyses of all data, by season and by year of age, bivariate analyses be- tween pairs of seasons and ages (2 to 6), and between traits were done. Estimates of heritability and repeat- ability over all ages were 0.49, 0.54, 0.68, and 0.16, and 0.65, 0.67, 0.75, and 0.30 for CW, WA, CH, and CS, respectively. Corresponding estimates for each age and season were similar for all traits and cycles. Estimates of genetic and permanent environmental correlations were close to unity for all pairs of seasons and traits. Genetic correlations were greater than 0.92 for all pairs of ages for CW, WA, and CH, and greater than 0.67 for CS. Genetic correlations were 0.80, 0.86, 0.43, and −0.04 for CW-CH, WA-CH, CW-CS, and CH-CS, respectively. Results suggest that repeatability models can be used to model weights and heights in this population.