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Naveed S, Toyinbo J, Ingole H, Valavanur Shekar P, Jones M, Campbell BT, Rustgi S. Development of High-Yielding Upland Cotton Genotypes with Reduced Regrowth after Defoliation Using a Combination of Molecular and Conventional Approaches. Genes (Basel) 2023; 14:2081. [PMID: 38003024 PMCID: PMC10671241 DOI: 10.3390/genes14112081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 11/12/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
Cotton is an economically important crop. However, the yield gain in cotton has stagnated over the years, probably due to its narrow genetic base. The introgression of beneficial variations through conventional and molecular approaches has helped broaden its genetic base to some extent. The growth habit of cotton is one of the crucial factors that determine crop maturation time, yield, and management. This study used 44 diverse upland cotton genotypes to develop high-yielding cotton germplasm with reduced regrowth after defoliation and early maturity by altering its growth habit from perennial to somewhat annual. We selected eight top-scoring genotypes based on the gene expression analysis of five floral induction and meristem identity genes (FT, SOC1, LFY, FUL, and AP1) and used them to make a total of 587 genetic crosses in 30 different combinations of these genotypes. High-performance progeny lines were selected based on the phenotypic data on plant height, flower and boll numbers per plant, boll opening date, floral clustering, and regrowth after defoliation as surrogates of annual growth habit, collected over four years (2019 to 2022). Of the selected lines, 8×5-B3, 8×5-B4, 9×5-C1, 8×9-E2, 8×9-E3, and 39×5-H1 showed early maturity, and 20×37-K1, 20×37-K2, and 20×37-D1 showed clustered flowering, reduced regrowth, high quality of fiber, and high lint yield. In 2022, 15 advanced lines (F8/F7) from seven cross combinations were selected and sent for an increase to a Costa Rica winter nursery to be used in advanced testing and for release as germplasm lines. In addition to these breeding lines, we developed molecular resources to breed for reduced regrowth after defoliation and improved yield by converting eight expression-trait-associated SNP markers we identified earlier into a user-friendly allele-specific PCR-based assay and tested them on eight parental genotypes and an F2 population.
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Affiliation(s)
- Salman Naveed
- Department of Plant and Environmental Sciences, Clemson University Pee Dee Research and Education Center, Florence, SC 29506, USA; (S.N.); (J.T.); (H.I.); (P.V.S.); (M.J.)
- USDA-ARS Southern Regional Research Center, New Orleans, LA 70124, USA
| | - Johnson Toyinbo
- Department of Plant and Environmental Sciences, Clemson University Pee Dee Research and Education Center, Florence, SC 29506, USA; (S.N.); (J.T.); (H.I.); (P.V.S.); (M.J.)
| | - Hrishikesh Ingole
- Department of Plant and Environmental Sciences, Clemson University Pee Dee Research and Education Center, Florence, SC 29506, USA; (S.N.); (J.T.); (H.I.); (P.V.S.); (M.J.)
| | - Prasanna Valavanur Shekar
- Department of Plant and Environmental Sciences, Clemson University Pee Dee Research and Education Center, Florence, SC 29506, USA; (S.N.); (J.T.); (H.I.); (P.V.S.); (M.J.)
| | - Michael Jones
- Department of Plant and Environmental Sciences, Clemson University Pee Dee Research and Education Center, Florence, SC 29506, USA; (S.N.); (J.T.); (H.I.); (P.V.S.); (M.J.)
| | - B. Todd Campbell
- USDA-ARS Coastal Plains Soil, Water, and Plant Research Center, Florence, SC 29501, USA;
| | - Sachin Rustgi
- Department of Plant and Environmental Sciences, Clemson University Pee Dee Research and Education Center, Florence, SC 29506, USA; (S.N.); (J.T.); (H.I.); (P.V.S.); (M.J.)
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Naveed S, Gandhi N, Billings G, Jones Z, Campbell BT, Jones M, Rustgi S. Alterations in Growth Habit to Channel End-of-Season Perennial Reserves towards Increased Yield and Reduced Regrowth after Defoliation in Upland Cotton ( Gossypium hirsutum L.). Int J Mol Sci 2023; 24:14174. [PMID: 37762483 PMCID: PMC10532291 DOI: 10.3390/ijms241814174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/03/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
Cotton (Gossypium spp.) is the primary source of natural textile fiber in the U.S. and a major crop in the Southeastern U.S. Despite constant efforts to increase the cotton fiber yield, the yield gain has stagnated. Therefore, we undertook a novel approach to improve the cotton fiber yield by altering its growth habit from perennial to annual. In this effort, we identified genotypes with high-expression alleles of five floral induction and meristem identity genes (FT, SOC1, FUL, LFY, and AP1) from an Upland cotton mini-core collection and crossed them in various combinations to develop cotton lines with annual growth habit, optimal flowering time, and enhanced productivity. To facilitate the characterization of genotypes with the desired combinations of stacked alleles, we identified molecular markers associated with the gene expression traits via genome-wide association analysis using a 63 K SNP Array. Over 14,500 SNPs showed polymorphism and were used for association analysis. A total of 396 markers showed associations with expression traits. Of these 396 markers, 159 were mapped to genes, 50 to untranslated regions, and 187 to random genomic regions. Biased genomic distribution of associated markers was observed where more trait-associated markers mapped to the cotton D sub-genome. Many quantitative trait loci coincided at specific genomic regions. This observation has implications as these traits could be bred together. The analysis also allowed the identification of candidate regulators of the expression patterns of these floral induction and meristem identity genes whose functions will be validated.
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Affiliation(s)
- Salman Naveed
- Department of Plant and Environmental Sciences, Clemson University Pee Dee Research and Education Center, Florence, SC 29506, USA; (S.N.); (M.J.)
| | - Nitant Gandhi
- Department of Plant and Environmental Sciences, Clemson University Pee Dee Research and Education Center, Florence, SC 29506, USA; (S.N.); (M.J.)
| | - Grant Billings
- Department of Crop & Soil Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Zachary Jones
- Department of Plant and Environmental Sciences, Clemson University Pee Dee Research and Education Center, Florence, SC 29506, USA; (S.N.); (M.J.)
| | - B. Todd Campbell
- USDA-ARS Coastal Plains Soil, Water, and Plant Research Center, Florence, SC 29501, USA;
| | - Michael Jones
- Department of Plant and Environmental Sciences, Clemson University Pee Dee Research and Education Center, Florence, SC 29506, USA; (S.N.); (M.J.)
| | - Sachin Rustgi
- Department of Plant and Environmental Sciences, Clemson University Pee Dee Research and Education Center, Florence, SC 29506, USA; (S.N.); (M.J.)
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Billings GT, Jones MA, Rustgi S, Bridges WC, Holland JB, Hulse-Kemp AM, Campbell BT. Outlook for Implementation of Genomics-Based Selection in Public Cotton Breeding Programs. Plants 2022; 11:plants11111446. [PMID: 35684219 PMCID: PMC9182660 DOI: 10.3390/plants11111446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/09/2022] [Accepted: 05/16/2022] [Indexed: 11/16/2022]
Abstract
Researchers have used quantitative genetics to map cotton fiber quality and agronomic performance loci, but many alleles may be population or environment-specific, limiting their usefulness in a pedigree selection, inbreeding-based system. Here, we utilized genotypic and phenotypic data on a panel of 80 important historical Upland cotton (Gossypium hirsutum L.) lines to investigate the potential for genomics-based selection within a cotton breeding program’s relatively closed gene pool. We performed a genome-wide association study (GWAS) to identify alleles correlated to 20 fiber quality, seed composition, and yield traits and looked for a consistent detection of GWAS hits across 14 individual field trials. We also explored the potential for genomic prediction to capture genotypic variation for these quantitative traits and tested the incorporation of GWAS hits into the prediction model. Overall, we found that genomic selection programs for fiber quality can begin immediately, and the prediction ability for most other traits is lower but commensurate with heritability. Stably detected GWAS hits can improve prediction accuracy, although a significance threshold must be carefully chosen to include a marker as a fixed effect. We place these results in the context of modern public cotton line-breeding and highlight the need for a community-based approach to amass the data and expertise necessary to launch US public-sector cotton breeders into the genomics-based selection era.
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Affiliation(s)
- Grant T. Billings
- Bioinformatics Graduate Program, North Carolina State University, Raleigh, NC 27695, USA; (G.T.B.); (J.B.H.)
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Michael A. Jones
- Pee Dee Research and Education Center, Clemson University, Florence, SC 29506, USA; (M.A.J.); (S.R.)
| | - Sachin Rustgi
- Pee Dee Research and Education Center, Clemson University, Florence, SC 29506, USA; (M.A.J.); (S.R.)
| | - William C. Bridges
- Department of Mathematical and Statistical Sciences, Clemson University, Clemson, SC 29634, USA;
| | - James B. Holland
- Bioinformatics Graduate Program, North Carolina State University, Raleigh, NC 27695, USA; (G.T.B.); (J.B.H.)
- Plant Sciences Research Unit, The Agricultural Research Service of U.S. Department of Agriculture, Raleigh, NC 27695, USA
| | - Amanda M. Hulse-Kemp
- Bioinformatics Graduate Program, North Carolina State University, Raleigh, NC 27695, USA; (G.T.B.); (J.B.H.)
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695, USA
- Genomics and Bioinformatics Research Unit, The Agricultural Research Service of U.S. Department of Agriculture, Raleigh, NC 27965, USA
- Correspondence: (A.M.H.-K.); (B.T.C.)
| | - B. Todd Campbell
- Coastal Plains Soil, Water, and Plant Research Center, The Agricultural Research Service of U.S. Department of Agriculture, Florence, SC 29501, USA
- Correspondence: (A.M.H.-K.); (B.T.C.)
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Jung S, Lee T, Gasic K, Campbell BT, Yu J, Humann J, Ru S, Edge-Garza D, Hough H, Main D. The Breeding Information Management System (BIMS): an online resource for crop breeding. Database (Oxford) 2021; 2021:6355633. [PMID: 34415997 PMCID: PMC8378516 DOI: 10.1093/database/baab054] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/14/2021] [Accepted: 08/09/2021] [Indexed: 11/17/2022]
Abstract
In this era of big data, breeding programs are producing ever larger amounts of data. This necessitates access to efficient management systems to keep track of cross, performance, pedigree, geographical and image-based data, as well as genotyping data. In this article, we report the progress on the Breeding Information Management System (BIMS), a free, secure and online breeding management system that allows breeders to store, manage, archive and analyze their private breeding data. BIMS is the first publicly available database system that enables individual breeders to integrate their private phenotypic and genotypic data with public data and, at the same time, have complete control of their own breeding data along with access to tools such as data import/export, data analysis and data archiving. The integration of breeding data with publicly available genomic and genetic data enhances genetic understanding of important traits and maximizes the marker-assisted breeding utility for breeders and allied scientists. BIMS incorporates the use of the Android App Field Book, open-source phenotype data collection software for phones and tablets that allows breeders to replace hard copy field books, thus alleviating the possibility of transcription errors while providing faster access to the collected data. BIMS comes with training materials and support for individual or small group training and is currently implemented in the Genome Database for Rosaceae, CottonGEN, the Citrus Genome Database, the Pulse Crop Database, and the Genome Database for Vaccinium. Database URLs: (https://www.rosaceae.org/), (https://www.cottongen.org/), (https://www.citrusgenomedb.org/), (https://www.pulsedb.org/) and (https://www.vaccinium.org/)
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Affiliation(s)
- Sook Jung
- Department of Horticulture, Washington State University, 45 Johnson Hall, Pullman, WA 99164, USA
| | - Taein Lee
- Department of Horticulture, Washington State University, 45 Johnson Hall, Pullman, WA 99164, USA
| | - Ksenija Gasic
- Plant and Environmental Sciences Department, 171 Poole Agricultural Center, Clemson University, Clemson, SC 29634, USA
| | - B Todd Campbell
- Coastal Plains Soil, Water, and Plant Research Center, USDA-ARS, 2611 West Lucas St., Florence, SC 29501-1242, USA
| | - Jing Yu
- Department of Horticulture, Washington State University, 45 Johnson Hall, Pullman, WA 99164, USA
| | - Jodi Humann
- Department of Horticulture, Washington State University, 45 Johnson Hall, Pullman, WA 99164, USA
| | - Sushan Ru
- Department of Horticulture, University of Auburn, 287 CASIC Building/120 Funchess, Auburn, AL 36849, USA
| | - Daniel Edge-Garza
- Centre for Horticultural Science, The University of Queensland, Brisbane St Lucia, Brisbane, QLD 4072, Australia
| | - Heidi Hough
- Department of Horticulture, Washington State University, 45 Johnson Hall, Pullman, WA 99164, USA
| | - Dorrie Main
- Department of Horticulture, Washington State University, 45 Johnson Hall, Pullman, WA 99164, USA
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Billings GT, Jones MA, Rustgi S, Hulse-Kemp AM, Campbell BT. Population structure and genetic diversity of the Pee Dee cotton breeding program. G3 (Bethesda) 2021; 11:jkab145. [PMID: 33914887 PMCID: PMC8495920 DOI: 10.1093/g3journal/jkab145] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 04/19/2021] [Indexed: 11/12/2022]
Abstract
Accelerated marker-assisted selection and genomic selection breeding systems require genotyping data to select the best parents for combining beneficial traits. Since 1935, the Pee Dee (PD) cotton germplasm enhancement program has developed an important genetic resource for upland cotton (Gossypium hirsutum L.), contributing alleles for improved fiber quality, agronomic performance, and genetic diversity. To date, a detailed genetic survey of the program's eight historical breeding cycles has yet to be undertaken. The objectives of this study were to evaluate genetic diversity across and within-breeding groups, examine population structure, and contextualize these findings relative to the global upland cotton gene pool. The CottonSNP63K array was used to identify 17,441 polymorphic markers in a panel of 114 diverse PD genotypes. A subset of 4597 markers was selected to decrease marker density bias. Identity-by-state pairwise distance varied substantially, ranging from 0.55 to 0.97. Pedigree-based estimates of relatedness were not very predictive of observed genetic similarities. Few rare alleles were present, with 99.1% of SNP alleles appearing within the first four breeding cycles. Population structure analysis with principal component analysis, discriminant analysis of principal components, fastSTRUCTURE, and a phylogenetic approach revealed an admixed population with moderate substructure. A small core collection (n < 20) captured 99% of the program's allelic diversity. Allele frequency analysis indicated potential selection signatures associated with stress resistance and fiber cell growth. The results of this study will steer future utilization of the program's germplasm resources and aid in combining program-specific beneficial alleles and maintaining genetic diversity.
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Affiliation(s)
- Grant T Billings
- Clemson University, Pee Dee Research and Education Center, Florence, SC 29501, USA
- North Carolina State University, Crop Science Department, Raleigh, NC 27695, USA
| | - Michael A Jones
- Clemson University, Pee Dee Research and Education Center, Florence, SC 29501, USA
| | - Sachin Rustgi
- Clemson University, Pee Dee Research and Education Center, Florence, SC 29501, USA
| | - Amanda M Hulse-Kemp
- North Carolina State University, Crop Science Department, Raleigh, NC 27695, USA
- USDA-ARS, Genomics and Bioinformatics Research Unit, Raleigh, NC 27695, USA
| | - B Todd Campbell
- USDA-ARS, Coastal Plains, Soil, Water, and Plant Research Center, Florence, SC 29501, USA
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Thyssen GN, Jenkins JN, McCarty JC, Zeng L, Campbell BT, Delhom CD, Islam MS, Li P, Jones DC, Condon BD, Fang DD. Whole genome sequencing of a MAGIC population identified genomic loci and candidate genes for major fiber quality traits in upland cotton (Gossypium hirsutum L.). Theor Appl Genet 2019; 132:989-999. [PMID: 30506522 DOI: 10.1007/s00122-018-3254-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 11/27/2018] [Indexed: 05/25/2023]
Abstract
Significant associations between candidate genes and six major cotton fiber quality traits were identified in a MAGIC population using GWAS and whole genome sequencing. Upland cotton (Gossypium hirsutum L.) is the world's major renewable source of fibers for textiles. To identify causative genetic variants that influence the major agronomic measures of cotton fiber quality, which are used to set discount or premium prices on each bale of cotton in the USA, we measured six fiber phenotypes from twelve environments, across three locations and 7 years. Our 550 recombinant inbred lines were derived from a multi-parent advanced generation intercross population and were whole-genome-sequenced at 3× coverage, along with the eleven parental cultivars at 20× coverage. The segregation of 473,517 single nucleotide polymorphisms (SNPs) in this population, including 7506 non-synonymous mutations, was combined with phenotypic data to identify seven highly significant fiber quality loci. At these loci, we found fourteen genes with non-synonymous SNPs. Among these loci, some had simple additive effects, while others were only important in a subset of the population. We observed additive effects for elongation and micronaire, when the three most significant loci for each trait were examined. In an informative subset where the major multi-trait locus on chromosome A07:72-Mb was fixed, we unmasked the identity of another significant fiber strength locus in gene Gh_D13G1792 on chromosome D13. The micronaire phenotype only revealed one highly significant genetic locus at one environmental location, demonstrating a significant genetic by environment component. These loci and candidate causative variant alleles will be useful to cotton breeders for marker-assisted selection with minimal linkage drag and potential biotechnological applications.
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Affiliation(s)
- Gregory N Thyssen
- Cotton Fiber Bioscience Research Unit, USDA-ARS-SRRC, New Orleans, LA, 70124, USA
- Cotton Chemistry and Utilization Unit, USDA-ARS-SRRC, New Orleans, LA, 70124, USA
| | - Johnie N Jenkins
- Genetics and Sustainable Agriculture Research Unit, USDA-ARS, Mississippi State, MS, 39762, USA
| | - Jack C McCarty
- Genetics and Sustainable Agriculture Research Unit, USDA-ARS, Mississippi State, MS, 39762, USA
| | - Linghe Zeng
- Crop Genetics Research Unit, USDA-ARS, Stoneville, MS, 38776, USA
| | - B Todd Campbell
- Coastal Plain Soil, Water and Plant Conservation Research Unit, USDA-ARS, Florence, SC, 29501, USA
| | - Christopher D Delhom
- Cotton Structure and Quality Research Unit, USDA-ARS-SRRC, New Orleans, LA, 70124, USA
| | - Md Sariful Islam
- Sugarcane Production Research Unit, USDA-ARS, Canal Point, FL, 33438, USA
| | - Ping Li
- Cotton Fiber Bioscience Research Unit, USDA-ARS-SRRC, New Orleans, LA, 70124, USA
| | | | - Brian D Condon
- Cotton Chemistry and Utilization Unit, USDA-ARS-SRRC, New Orleans, LA, 70124, USA
| | - David D Fang
- Cotton Fiber Bioscience Research Unit, USDA-ARS-SRRC, New Orleans, LA, 70124, USA.
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Yang Y, Ferreira G, Corl BA, Campbell BT. Production performance, nutrient digestibility, and milk fatty acid profile of lactating dairy cows fed corn silage- or sorghum silage-based diets with and without xylanase supplementation. J Dairy Sci 2019; 102:2266-2274. [PMID: 30639005 DOI: 10.3168/jds.2018-15801] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 11/27/2018] [Indexed: 11/19/2022]
Abstract
The objective of this study was to evaluate the effects of supplementing xylanase on production performance, nutrient digestibility, and milk fatty acid profile in high-producing dairy cows consuming corn silage- or sorghum silage-based diets. Conventional corn (80,000 seeds/ha) and brown midrib forage sorghum (250,000 seeds/ha) were planted, harvested [34 and 32% of dry matter (DM), respectively], and ensiled for more than 10 mo. Four primiparous and 20 multiparous Holstein cows were randomly assigned to 1 of 4 diets in a replicated 4 × 4 Latin square design with a 2 × 2 factorial arrangement of treatments and 19-d periods. Treatment diets consisted of (1) corn silage-based diet without xylanase, (2) corn silage-based diet with xylanase, (3) sorghum silage-based diet without xylanase, and (4) sorghum silage-based diet with xylanase. The xylanase product was supplemented at a rate of 1.5 g of product/kg of total DM. Corn silage had higher concentrations of starch (31.2 vs. 29.2%), slightly higher concentrations of crude protein (7.1 vs. 6.8%) and fat (3.7 vs. 3.2%), and lower concentrations of neutral detergent fiber (36.4 vs. 49.0%) and lignin (2.1 vs. 5.7%) than sorghum silage. Xylanase supplementation did not affect DM intake, milk yield, milk fat percentage and yield, milk protein percentage and yield, lactose percentage and yield, and 3.5% fat-corrected milk yield. Cows consuming corn silage-based diets consumed 13% more DM (28.8 vs. 25.5 kg/d) and produced 5% more milk (51.6 vs. 48.9 kg/d) than cows consuming sorghum silage-based diets. Milk from cows consuming sorghum silage-based diets had 16% greater fat concentrations (3.84 and 3.30%) than milk from cows consuming corn silage-based diets. This resulted in 8% greater fat yields (1.81 vs. 1.68 kg/d). Silage type did not affect milk protein and lactose concentrations. Xylanase supplementation did not affect nutrient digestibility. Cows consuming corn silage-based diets showed greater DM (77.3 vs. 73.5%), crude protein (78.0 vs. 72.4), and starch (99.2 vs. 96.5%) digestibilities than cows consuming sorghum silage-based diets. In conclusion, xylanase supplementation did not improve production performance when high-producing dairy cows were fed corn silage- or sorghum silage-based diets. In addition, production performance can be sustained by feeding sorghum silage in replacement of corn silage.
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Affiliation(s)
- Y Yang
- Department of Dairy Science, Virginia Tech, Blacksburg 24060
| | - G Ferreira
- Department of Dairy Science, Virginia Tech, Blacksburg 24060.
| | - B A Corl
- Department of Dairy Science, Virginia Tech, Blacksburg 24060
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Hagadorn JI, Brownell EA, Herbst KW, Trzaski JM, Neff S, Campbell BT. Trends in treatment and in-hospital mortality for neonates with congenital diaphragmatic hernia. J Perinatol 2015; 35:748-54. [PMID: 25950919 DOI: 10.1038/jp.2015.46] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 02/14/2015] [Accepted: 03/04/2015] [Indexed: 01/05/2023]
Abstract
OBJECTIVE We performed a retrospective cohort study in order to examine recent trends in use of post-partum treatments and in-hospital mortality for congenital diaphragmatic hernia (CDH). STUDY DESIGN Included were infants with CDH, born in 2003 to 2012 and hospitalized at ⩽7 days of age at one of 33 United States tertiary referral children's hospitals with extracorporeal membrane oxygenation (ECMO) programs. In-hospital mortality as well as use of ECMO, surfactant and a variety of vasodilators were examined for trends during the study period. RESULT Inclusion criteria were met by 3123 infants with CDH. Among 2423 term or near-term infants, odds of death decreased annually for those with isolated or complex CDH. For 700 premature or low-birth weight infants with CDH, in-hospital mortality did not change. Among treatments for CDH, increasing with time in the study cohort were use of milrinone and sildenafil individually, and use of multiple vasodilators during the hospitalization. CONCLUSION Survival improved in large subgroups of term or near-term infants with CDH in this 10-year multicenter cohort, temporally associated with increasing use of multiple vasodilators. Use of vasodilators for infants with CDH is increasing despite a lack of evidence supporting efficacy or safety. Prospective research is needed to clarify specific causal effects contributing to improving survival in these infants.
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Affiliation(s)
- J I Hagadorn
- Division of Neonatology, Department of Pediatrics, University of Connecticut School of Medicine, Farmington, CT, USA
| | - E A Brownell
- Division of Neonatology, Department of Pediatrics, University of Connecticut School of Medicine, Farmington, CT, USA
| | - K W Herbst
- Departments of Pediatric Urology and Research, Connecticut Children's Medical Center, Hartford, CT, USA
| | - J M Trzaski
- Division of Neonatology, Department of Pediatrics, University of Connecticut School of Medicine, Farmington, CT, USA
| | - S Neff
- Departments of Pediatric Urology and Research, Connecticut Children's Medical Center, Hartford, CT, USA
| | - B T Campbell
- Department of Pediatric Surgery, Connecticut Children's Medical Center, Hartford, CT, USA
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Campbell BT, Kojima CJ, Cooper TA, Bastin BC, Wojakiewicz L, Kallenbach RL, Schrick FN, Waller JC. A single nucleotide polymorphism in the dopamine receptor D2 gene may be informative for resistance to fescue toxicosis in angus-based cattle. Anim Biotechnol 2014; 25:1-12. [PMID: 24299180 DOI: 10.1080/10495398.2013.796960] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Fescue toxicosis (FT) reduces beef animal growth and fertility. Animals afflicted with FT typically have decreased circulating prolactin concentrations and thicker summer hair coats. Preliminary experiments examined the informativeness of a novel Dopamine Receptor 2 (DRD2) G/A SNP for resistance to FT. Steers grazed tall fescue containing a toxic (E+) or non-toxic (NTE) strain of endophyte. Decreased serum prolactin concentrations were observed in GG steers in May compared to AA steers when grazing E+ pastures (P < 0.02). In a second study, GG steers had decreased prolactin concentrations (P = 0.004) and increased hair coat scores (P = 0.01) relative to AA steers when grazing E+ pastures. Allele and genotypic frequencies were different (P = 0.016 and 0.026, respectively) between spring-calving and fall-calving herds grazing E+ pastures, such that the A allele and the AA genotype were more prevalent in spring-calving herds, suggesting active selection for the A allele. Regardless of calving season, AA heifers tended toward fewer days to first calf (733.6 ± 4.4 d) than did GG heifers (756.6 ± 9.2 days; P = 0.055). These results suggest that the DRD2 SNP may have use in selecting animals resistant to FT.
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Affiliation(s)
- B T Campbell
- a Department of Animal Science , University of Tennessee , Knoxville , Tennessee , USA
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Tyagi P, Gore MA, Bowman DT, Campbell BT, Udall JA, Kuraparthy V. Genetic diversity and population structure in the US Upland cotton (Gossypium hirsutum L.). Theor Appl Genet 2014; 127:283-95. [PMID: 24170350 DOI: 10.1007/s00122-013-2217-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Accepted: 10/14/2013] [Indexed: 05/09/2023]
Abstract
Genetic diversity and population structure in the US Upland cotton was established and core sets of allelic richness were identified for developing association mapping populations in cotton. Elite plant breeding programs could likely benefit from the unexploited standing genetic variation of obsolete cultivars without the yield drag typically associated with wild accessions. A set of 381 accessions comprising 378 Upland (Gossypium hirsutum L.) and 3 G. barbadense L. accessions of the United States cotton belt were genotyped using 120 genome-wide SSR markers to establish the genetic diversity and population structure in tetraploid cotton. These accessions represent more than 100 years of Upland cotton breeding in the United States. Genetic diversity analysis identified a total of 546 alleles across 141 marker loci. Twenty-two percent of the alleles in Upland accessions were unique, specific to a single accession. Population structure analysis revealed extensive admixture and identified five subgroups corresponding to Southeastern, Midsouth, Southwest, and Western zones of cotton growing areas in the United States, with the three accessions of G. barbadense forming a separate cluster. Phylogenetic analysis supported the subgroups identified by STRUCTURE. Average genetic distance between G. hirsutum accessions was 0.195 indicating low levels of genetic diversity in Upland cotton germplasm pool. The results from both population structure and phylogenetic analysis were in agreement with pedigree information, although there were a few exceptions. Further, core sets of different sizes representing different levels of allelic richness in Upland cotton were identified. Establishment of genetic diversity, population structure, and identification of core sets from this study could be useful for genetic and genomic analysis and systematic utilization of the standing genetic variation in Upland cotton.
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Affiliation(s)
- Priyanka Tyagi
- Crop Science Department, North Carolina State University, Raleigh, NC, 27695, USA
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Bowman MJ, Park W, Bauer PJ, Udall JA, Page JT, Raney J, Scheffler BE, Jones DC, Campbell BT. RNA-Seq transcriptome profiling of upland cotton (Gossypium hirsutum L.) root tissue under water-deficit stress. PLoS One 2013; 8:e82634. [PMID: 24324815 PMCID: PMC3855774 DOI: 10.1371/journal.pone.0082634] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2013] [Accepted: 11/04/2013] [Indexed: 11/19/2022] Open
Abstract
An RNA-Seq experiment was performed using field grown well-watered and naturally rain fed cotton plants to identify differentially expressed transcripts under water-deficit stress. Our work constitutes the first application of the newly published diploid D5 Gossypium raimondii sequence in the study of tetraploid AD1 upland cotton RNA-seq transcriptome analysis. A total of 1,530 transcripts were differentially expressed between well-watered and water-deficit stressed root tissues, in patterns that confirm the accuracy of this technique for future studies in cotton genomics. Additionally, putative sequence based genome localization of differentially expressed transcripts detected A2 genome specific gene expression under water-deficit stress. These data will facilitate efforts to understand the complex responses governing transcriptomic regulatory mechanisms and to identify candidate genes that may benefit applied plant breeding programs.
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Affiliation(s)
- Megan J. Bowman
- USDA-ARS, Coastal Plains Soil, Water and Plant Research Center, Florence, South Carolina, United States of America
| | - Wonkeun Park
- USDA-ARS, Coastal Plains Soil, Water and Plant Research Center, Florence, South Carolina, United States of America
- Clemson University Pee Dee Research and Education Center, Florence, South Carolina, United States of America
| | - Philip J. Bauer
- USDA-ARS, Coastal Plains Soil, Water and Plant Research Center, Florence, South Carolina, United States of America
| | - Joshua A. Udall
- Brigham Young University, Provo, Utah, United States of America
| | - Justin T. Page
- Brigham Young University, Provo, Utah, United States of America
| | - Joshua Raney
- Brigham Young University, Provo, Utah, United States of America
| | | | - Don. C. Jones
- Cotton Incorporated, Agricultural and Environmental Research, Cary, North Carolina, United States of America
| | - B. Todd Campbell
- USDA-ARS, Coastal Plains Soil, Water and Plant Research Center, Florence, South Carolina, United States of America
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Rustgi S, Shafqat MN, Kumar N, Baenziger PS, Ali ML, Dweikat I, Campbell BT, Gill KS. Genetic dissection of yield and its component traits using high-density composite map of wheat chromosome 3A: bridging gaps between QTLs and underlying genes. PLoS One 2013; 8:e70526. [PMID: 23894667 PMCID: PMC3722237 DOI: 10.1371/journal.pone.0070526] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 06/25/2013] [Indexed: 11/18/2022] Open
Abstract
Earlier we identified wheat (Triticum aestivum L.) chromosome 3A as a major determinant of grain yield and its component traits. In the present study, a high-density genetic linkage map of 81 chromosome 3A-specific markers was developed to increase the precision of previously identified yield component QTLs, and to map QTLs for biomass-related traits. Many of the previously identified QTLs for yield and its component traits were confirmed and were localized to narrower intervals. Four novel QTLs one each for shoot biomass (Xcfa2262-Xbcd366), total biomass (wPt2740-Xcfa2076), kernels/spike (KPS) (Xwmc664-Xbarc67), and Pseudocercosporella induced lodging (PsIL) were also detected. The major QTLs identified for grain yield (GY), KPS, grain volume weight (GVWT) and spikes per square meter (SPSM) respectively explained 23.2%, 24.2%, 20.5% and 20.2% of the phenotypic variation. Comparison of the genetic map with the integrated physical map allowed estimation of recombination frequency in the regions of interest and suggested that QTLs for grain yield detected in the marker intervals Xcdo549-Xbarc310 and Xpsp3047-Xbarc356 reside in the high-recombination regions, thus should be amenable to map-based cloning. On the other hand, QTLs for KPS and SPSM flanked by markers Xwmc664 and Xwmc489 mapped in the low-recombination region thus are not suitable for map-based cloning. Comparisons with the rice (Oryza sativa L.) genomic DNA sequence identified 11 candidate genes (CGs) for yield and yield related QTLs of which chromosomal location of two (CKX2 and GID2-like) was confirmed using wheat aneuploids. This study provides necessary information to perform high-resolution mapping for map-based cloning and for CG-based cloning of yield QTLs.
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Affiliation(s)
- Sachin Rustgi
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, United States of America
| | - Mustafa N. Shafqat
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, United States of America
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Neeraj Kumar
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, United States of America
| | - P. Stephen Baenziger
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - M. Liakat Ali
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Ismail Dweikat
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - B. Todd Campbell
- Agricultural Research Service, Coastal Plains Soil, Water, and Plant Research Center, Florence, South Carolina, United States of America
| | - Kulvinder Singh Gill
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, United States of America
- * E-mail:
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Park W, Scheffler BE, Bauer PJ, Campbell BT. Genome-wide identification of differentially expressed genes under water deficit stress in upland cotton (Gossypium hirsutum L.). BMC Plant Biol 2012; 12:90. [PMID: 22703539 PMCID: PMC3438127 DOI: 10.1186/1471-2229-12-90] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Accepted: 05/10/2012] [Indexed: 05/17/2023]
Abstract
BACKGROUND Cotton is the world's primary fiber crop and is a major agricultural commodity in over 30 countries. Like many other global commodities, sustainable cotton production is challenged by restricted natural resources. In response to the anticipated increase of agricultural water demand, a major research direction involves developing crops that use less water or that use water more efficiently. In this study, our objective was to identify differentially expressed genes in response to water deficit stress in cotton. A global expression analysis using cDNA-Amplified Fragment Length Polymorphism was conducted to compare root and leaf gene expression profiles from a putative drought resistant cotton cultivar grown under water deficit stressed and well watered field conditions. RESULTS We identified a total of 519 differentially expressed transcript derived fragments. Of these, 147 transcript derived fragment sequences were functionally annotated according to their gene ontology. Nearly 70 percent of transcript derived fragments belonged to four major categories: 1) unclassified, 2) stress/defense, 3) metabolism, and 4) gene regulation. We found heat shock protein-related and reactive oxygen species-related transcript derived fragments to be among the major parts of functional pathways induced by water deficit stress. Also, twelve novel transcripts were identified as both water deficit responsive and cotton specific. A subset of differentially expressed transcript derived fragments was verified using reverse transcription-polymerase chain reaction. Differential expression analysis also identified five pairs of duplicated transcript derived fragments in which four pairs responded differentially between each of their two homologues under water deficit stress. CONCLUSIONS In this study, we detected differentially expressed transcript derived fragments from water deficit stressed root and leaf tissues in tetraploid cotton and provided their gene ontology, functional/biological distribution, and possible roles of gene duplication. This discovery demonstrates complex mechanisms involved with polyploid cotton's transcriptome response to naturally occurring field water deficit stress. The genes identified in this study will provide candidate targets to manipulate the water use characteristics of cotton at the molecular level.
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Affiliation(s)
- Wonkeun Park
- USDA-ARS, Coastal Plains Soil, Water and Plant Research Center, Florence, SC, USA
| | | | - Philip J Bauer
- USDA-ARS, Coastal Plains Soil, Water and Plant Research Center, Florence, SC, USA
| | - B Todd Campbell
- USDA-ARS, Coastal Plains Soil, Water and Plant Research Center, Florence, SC, USA
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Horn PJ, Neogi P, Tombokan X, Ghosh S, Campbell BT, Chapman KD. Simultaneous Quantification of Oil and Protein in Cottonseed by Low-Field Time-Domain Nuclear Magnetic Resonance. J AM OIL CHEM SOC 2011. [DOI: 10.1007/s11746-011-1829-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Park W, Scheffler BE, Bauer PJ, Campbell BT. Identification of the family of aquaporin genes and their expression in upland cotton (Gossypium hirsutum L.). BMC Plant Biol 2010; 10:142. [PMID: 20626869 PMCID: PMC3095289 DOI: 10.1186/1471-2229-10-142] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Accepted: 07/13/2010] [Indexed: 05/18/2023]
Abstract
BACKGROUND Cotton (Gossypium spp.) is produced in over 30 countries and represents the most important natural fiber in the world. One of the primary factors affecting both the quantity and quality of cotton production is water. A major facilitator of water movement through cell membranes of cotton and other plants are the aquaporin proteins. Aquaporin proteins are present as diverse forms in plants, where they function as transport systems for water and other small molecules. The plant aquaporins belong to the large major intrinsic protein (MIP) family. In higher plants, they consist of five subfamilies including plasma membrane intrinsic proteins (PIP), tonoplast intrinsic proteins (TIP), NOD26-like intrinsic proteins (NIP), small basic intrinsic proteins (SIP), and the recently discovered X intrinsic proteins (XIP). Although a great deal is known about aquaporins in plants, very little is known in cotton. RESULTS From a molecular cloning effort, together with a bioinformatic homology search, 71 upland cotton (G. hirsutum) aquaporin genes were identified. The cotton aquaporins consist of 28 PIP and 23 TIP members with high sequence similarity. We also identified 12 NIP and 7 SIP members that showed more divergence. In addition, one XIP member was identified that formed a distinct 5th subfamily. To explore the physiological roles of these aquaporin genes in cotton, expression analyses were performed for a select set of aquaporin genes from each subfamily using semi-quantitative reverse transcription (RT)-PCR. Our results suggest that many cotton aquaporin genes have high sequence similarity and diverse roles as evidenced by analysis of sequences and their expression. CONCLUSION This study presents a comprehensive identification of 71 cotton aquaporin genes. Phylogenetic analysis of amino acid sequences divided the large and highly similar multi-gene family into the known 5 aquaporin subfamilies. Together with expression and bioinformatic analyses, our results support the idea that the genes identified in this study represent an important genetic resource providing potential targets to modify the water use properties of cotton.
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Affiliation(s)
- Wonkeun Park
- USDA-ARS, Coastal Plains Soil, Water and Plant Research Center, 2611 West Lucas St., Florence, 29501, SC, USA
| | - Brian E Scheffler
- USDA-ARS, MSA Genomics and Bioinformatics Research Unit, 141 Experiment Station Rd., Stoneville, 38776, MS, USA
| | - Philip J Bauer
- USDA-ARS, Coastal Plains Soil, Water and Plant Research Center, 2611 West Lucas St., Florence, 29501, SC, USA
| | - B Todd Campbell
- USDA-ARS, Coastal Plains Soil, Water and Plant Research Center, 2611 West Lucas St., Florence, 29501, SC, USA
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Dilbirligi M, Erayman M, Campbell BT, Randhawa HS, Baenziger PS, Dweikat I, Gill KS. High-density mapping and comparative analysis of agronomically important traits on wheat chromosome 3A. Genomics 2006; 88:74-87. [PMID: 16624516 DOI: 10.1016/j.ygeno.2006.02.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2005] [Revised: 01/13/2006] [Accepted: 02/05/2006] [Indexed: 11/27/2022]
Abstract
Bread wheat chromosome 3A has been shown to contain genes/QTLs controlling grain yield and other agronomic traits. The objectives of this study were to generate high-density physical and genetic-linkage maps of wheat homoeologous group 3 chromosomes and reveal the physical locations of genes/QTLs controlling yield and its component traits, as well as agronomic traits, to obtain a precise estimate of recombination for the corresponding regions and to enrich the QTL-containing regions with markers. Physical mapping was accomplished by 179 DNA markers mostly representing expressed genes using 41 single-break deletion lines. Polymorphism survey of cultivars Cheyenne (CNN) and Wichita (WI), and a substitution line of CNN carrying chromosome 3A from WI [CNN(WI3A)], with 142 RFLP probes and 55 SSR markers revealed that the extent of polymorphism is different among various group 3 chromosomal regions as well as among the homoeologs. A genetic-linkage map for chromosome 3A was developed by mapping 17 QTLs for seven agronomic traits relative to 26 RFLP and 15 SSR chromosome 3A-specific markers on 95 single-chromosome recombinant inbred lines. Comparison of the physical maps with the 3A genetic-linkage map localized the QTLs to gene-containing regions and accounted for only about 36% of the chromosome. Two chromosomal regions containing 9 of the 17 QTLs encompassed less than 10% of chromosome 3A but accounted for almost all of the arm recombination. To identify rice chromosomal regions corresponding to the particular QTL-containing wheat regions, 650 physically mapped wheat group 3 sequences were compared with rice genomic sequences. At an E value of E < or = 10(-5), 82% of the wheat group 3 sequences identified rice homologs, of which 54% were on rice chromosome 1. The rice chromosome 1 region collinear with the two wheat regions that contained 9 QTLs was about 6.5 Mb.
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Affiliation(s)
- Muharrem Dilbirligi
- Crop and Soil Science Department, Washington State University, P.O. Box 646420, 277 Johnson Hall, Pullman, WA 99164, USA
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