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1.
Commun Biol ; 5(1): 60, 2022 01 17.
Artigo em Inglês | MEDLINE | ID: mdl-35039628

RESUMO

Cotton (Gossypium hirsutum L.) fiber is the most important resource of natural and renewable fiber for the textile industry. However, the understanding of genetic components and their genome-wide interactions controlling fiber quality remains fragmentary. Here, we sequenced a multiple-parent advanced-generation inter-cross (MAGIC) population, consisting of 550 individuals created by inter-crossing 11 founders, and established a mosaic genome map through tracing the origin of haplotypes that share identity-by-descent (IBD). We performed two complementary GWAS methods-SNP-based GWAS (sGWAS) and IBD-based haplotype GWAS (hGWAS). A total of 25 sQTLs and 14 hQTLs related to cotton fiber quality were identified, of which 26 were novel QTLs. Two major QTLs detected by both GWAS methods were responsible for fiber strength and length. The gene Ghir_D11G020400 (GhZF14) encoding the MATE efflux family protein was identified as a novel candidate gene for fiber length. Beyond the additive QTLs, we detected prevalent epistatic interactions that contributed to the genetics of fiber quality, pinpointing another layer for trait variance. This study provides new targets for future molecular design breeding of superior fiber quality.


Assuntos
Fibra de Algodão/análise , Genoma de Planta , Gossypium/genética , Fenótipo , Locos de Características Quantitativas , Mapeamento Cromossômico , Estudo de Associação Genômica Ampla , Gossypium/crescimento & desenvolvimento
2.
Plants (Basel) ; 10(11)2021 Nov 13.
Artigo em Inglês | MEDLINE | ID: mdl-34834813

RESUMO

Palmer amaranth is a problematic common weed species, especially in cotton. With the wide use of chemical herbicide and herbicide-tolerant transgenic cotton lines, Palmer amaranth populations have developed tolerance to commonly used herbicides. It is imperative to develop alternative weed control methods to slow the evolution of herbicide-resistant weed populations and provide new strategies for weed management. Eleven chromosome substitution (CS) cotton lines (CS-B26lo, CS-T17, CS-B16-15, CS-B17-11, CS-B12, CS-T05sh, CS-T26lo, CS-T11sh, CS-M11sh, CS-B22sh, and CS-B22lo) were screened for weed-suppressing abilities in this study. The cotton lines were tested using the established stair-step assay. Height (cm) and chlorophyll concentration (cci) were measured for each plant in the system. The most significant variation in Palmer amaranth height reduction among the CS lines was observed 21 days after establishment. CS-B22sh (76.82%) and T26lo (68.32%) were most effective in reducing Palmer amaranth height. The cluster analysis revealed that CS-B22sh, and CS-T26lo were clustered in one group, suggesting similar genetic potential with reference to Palmer amaranth growth and development. CS-B22sh showed novel genetic potential to control the growth and development of Palmer amaranth, a problematic weed in cotton fields. Future experimentation should implement more parameters and chemical testing to explore allelopathic interactions among CS lines and Palmer amaranth.

3.
Plants (Basel) ; 10(6)2021 Jun 07.
Artigo em Inglês | MEDLINE | ID: mdl-34200224

RESUMO

Nutrients, including macronutrients such as Ca, P, K, and Mg, are essential for crop production and seed quality, and for human and animal nutrition and health. Macronutrient deficiencies in soil lead to poor crop nutritional qualities and a low level of macronutrients in cottonseed meal-based products, leading to malnutrition. Therefore, the discovery of novel germplasm with a high level of macronutrients or significant variability in the macronutrient content of crop seeds is critical. To our knowledge, there is no information available on the effects of chromosome or chromosome arm substitution on cottonseed macronutrient content. The objective of this study was to evaluate the effects of chromosome or chromosome arm substitution on the variability and content of the cottonseed macronutrients Ca, K, Mg, N, P, and S in chromosome substitution lines (CS). Nine chromosome substitution lines were grown in two-field experiments at two locations in 2013 in South Carolina, USA, and in 2014 in Mississippi, USA. The controls used were TM-1, the recurrent parent of the CS line, and the cultivar AM UA48. The results showed major variability in macronutrients among CS lines and between CS lines and controls. For example, in South Carolina, the mean values showed that five CS lines (CS-T02, CS-T04, CS-T08sh, CS-B02, and CS-B04) had higher Ca level in seed than controls. Ca levels in these CS lines varied from 1.88 to 2.63 g kg-1 compared with 1.81 and 1.72 g kg-1 for TM-1 and AMUA48, respectively, with CS-T04 having the highest Ca concentration. CS-M08sh exhibited the highest K concentration (14.50 g kg-1), an increase of 29% and 49% over TM-1 and AM UA48, respectively. Other CS lines had higher Mg, P, and S than the controls. A similar trend was found at the MS location. This research demonstrated that chromosome substitution resulted in higher seed macronutrients in some CS lines, and these CS lines with a higher content of macronutrients can be used as a genetic tool towards the identification of desired seed nutrition traits. Also, the CS lines with higher desired macronutrients can be used as parents to breed for improved nutritional quality in Upland cotton, Gossypium hirsutum L., through improvement by the interspecific introgression of desired seed nutrient traits such as Ca, K, P, S, and N. The positive and significant (p ≤ 0.0001) correlation of P with Ca, P with Mg, S with P, and S with N will aid in understanding the relationships between nutrients to improve the fertilizer management program and maintain higher cottonseed nutrient content.

4.
Mol Genet Genomics ; 296(1): 119-129, 2021 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-33051724

RESUMO

Cotton is grown in arid and semi-arid regions where abiotic stresses such as drought and salt are prevalent. There is a lack of studies that simultaneously address the genetic and genomic basis of tolerance to drought and salt stress. In this study, a multi-parent advanced generation inter-cross (MAGIC) population of 550 recombinant inbred lines (RILs) together with their 11 Upland cotton parents with a total of 473,516 polymorphic SNP markers was used to identify quantitative trait loci (QTL) for drought tolerance (DT) and salt tolerance (ST) at the seedling stage based on two replicated greenhouse tests. Transgressive segregation occurred in the MAGIC-RILs, indicating that tolerant and sensitive alleles recombined for tolerance to the abiotic stress during the intermating process for the population development. A total of 20 QTL were detected for DT including 13 and 7 QTL based on plant height (PH) and dry shoot weight (DSW), respectively; and 23 QTL were detected for ST including 12 and 11 QTL for PH and DSW, respectively. There were several chromosomes with QTL clusters for abiotic stress tolerance including four QTL on chromosome A13 and three QTL on A01 for DT, and four QTL on D08 and three QTL on A11 for ST. Nine QTL (21% of the 43 QTL) detected were in common between DT and ST, indicating a common genetic basis for DT and ST. The narrow chromosomal regions for most of the QTL detected in this study allowed identification of 53 candidate genes associated with responses to salt and drought stress and abiotic stimulus. The QTL identified for both DT and ST have significantly augmented the repertoire of QTL for abiotic stress tolerance that can be used for marker-assisted selection to develop cultivars with resilience to drought and/or salt and further genomic studies towards the identification of drought and salt tolerance genes in cotton.


Assuntos
Cromossomos de Plantas/química , Gossypium/genética , Locos de Características Quantitativas , Tolerância ao Sal/genética , Estresse Fisiológico/genética , Mapeamento Cromossômico , Fibra de Algodão/análise , Cruzamentos Genéticos , Secas , Marcadores Genéticos , Estudo de Associação Genômica Ampla , Gossypium/crescimento & desenvolvimento , Gossypium/metabolismo , Melhoramento Vegetal , Brotos de Planta/genética , Brotos de Planta/crescimento & desenvolvimento , Brotos de Planta/metabolismo , Salinidade , Plântula/genética , Plântula/crescimento & desenvolvimento , Plântula/metabolismo
5.
Plants (Basel) ; 9(12)2020 Dec 10.
Artigo em Inglês | MEDLINE | ID: mdl-33321878

RESUMO

Upland cotton (Gossypium hirsutum L.) growth and development during the pre-and post-flowering stages are susceptible to high temperature and drought. We report the field-based characterization of multiple morpho-physiological and reproductive stress resilience traits in 11 interspecific chromosome substitution (CS) lines isogenic to each other and the inbred G. hirsutum line TM-1. Significant genetic variability was detected (p < 0.001) in multiple traits in CS lines carrying chromosomes and chromosome segments from CS-B (G. barbadense) and CS-T (G. tomentosum). Line CS-T15sh had a positive effect on photosynthesis (13%), stomatal conductance (33%), and transpiration (24%), and a canopy 6.8 °C cooler than TM-1. The average pollen germination was approximately 8% greater among the CS-B than CS-T lines. Based on the stress response index, three CS lines are identified as heat- and drought-tolerant (CS-T07, CS-B15sh, and CS-B18). The three lines demonstrated enhanced photosynthesis (14%), stomatal conductance (29%), transpiration (13%), and pollen germination (23.6%) compared to TM-1 under field conditions, i.e., traits that would expectedly enhance performance in stressful environments. The generated phenotypic data and stress-tolerance indices on novel CS lines, along with phenotypic methods, would help in developing new cultivars with improved resilience to the effects of global warming.

6.
Plants (Basel) ; 9(9)2020 Aug 23.
Artigo em Inglês | MEDLINE | ID: mdl-32842514

RESUMO

Micronutrients are essential for plant growth and development, and important for human health nutrition and livestock feed. Therefore, the discovery of novel germplasm with significant variability or higher micronutrients content in crop seeds is critical. Currently, there is no information available on the effects of chromosome or chromosome arm substitution in cotton on cottonseed micronutrients. Thus, the objective of this study was to evaluate the effects of chromosome or chromosome arm substitution on the variability and levels of micronutrients B, Fe, Cu, Zn, Mn, and Ni in cottonseed from chromosome substitution (CS) cotton lines. Our hypothesis was that interspecific chromosome substitution in cotton can affect cottonseed micronutrients content, resulting in significant differences and variabilities of these nutrients among CS lines and between CS lines and the controls. Nine CS lines were grown in two-field experiments at two locations (in 2013 in South Carolina, USA; and in 2014 in Mississippi, USA). TM-1 (the recurrent parent of the CS line) and AM UA48 (cultivar) were used as control. The results showed significant variability among CS lines compared to the controls AM UA48 and TM-1. For example, in South Carolina (SC), B concentration in cottonseed ranged from 10.35 mg kg-1 in CS-M02 to 13.67 mg kg-1 in CS-T04. The concentration of Cu ranged from 4.81 mg kg-1 in CS-B08sh to 7.65 mg kg-1 in CS-T02, and CS-T02 was higher than both controls. The concentration of Fe ranged from 36.09 mg kg-1 to 56.69 mg kg-1 (an increase up to 57%), and six CS lines (CS-B02, CS-B08sh, CS-M02, CS-M04, CS-T02, and CS-T04) had higher concentration than both controls in 2013. In 2014 at the Mississippi location (MS), similar observation was found with CS lines for micronutrients content. The CS lines with higher concentrations of these micronutrients can be used as a genetic tool toward QTL identification for desired seed traits because these lines are genetically similar with TM-1, except the substituted chromosome or chromosome segment pairs from the alien species. Chromosome substitution provides an effective means for upland cotton improvement by targeted interspecific introgression, yielding CS lines that facilitate trait discovery, such as seed micronutritional qualities, due to increased isogenicity and markedly reduced complexity from epistatic interactions with non-target alien chromosomes. The positive correlation between B, Cu, and Fe at both locations, between Ni and Mn, between Zn and Cu, and between Zn and Ni at both locations signify the importance of a good agricultural and fertilizer management of these nutrients to maintain higher cottonseed nutrient content.

7.
Phytopathology ; 110(4): 927-932, 2020 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-31961253

RESUMO

Cotton (Gossypium hirsutum) resistance to root-knot nematode (RKN) (Meloidogyne incognita) is controlled by quantitative trait loci (QTLs) on chromosomes 11 (CHR11) and 14 (CHR14). The individual contributions of these QTLs to resistance are not completely understood. We developed near isogenic lines susceptible at both loci (null), having CHR11 or CHR14 alone, and having both QTLs (CHR11/CHR14). RKN reproduction, postinfection development, egg mass formation, and adult female fecundity were evaluated. Total RKN reproduction was reduced more in CHR14 versus CHR11 but not as greatly as in CHR11/CHR14. Second-stage juvenile (J2) development to the J3 and J4 (J3+J4) life stages was delayed in CHR11, whereas the J2 transition to J3+J4 in CHR14 followed a similar track as in null plants. Development of J3+J4 nematodes to adult females was inhibited in CHR14 at 21 days after inoculation (DAI). Adult female numbers were decreased in CHR11 and CHR14 at 21 and 28 DAI, with CHR11/CHR14 showing an even greater reduction by 28 DAI. The number of egg masses per gram of root at 21, 28, and 35 DAI formed on CHR11 and CHR14 followed a similar track as numbers of adult females. RKN adult female fecundity (eggs/egg mass) was reduced for CHR11 and CHR14 compared with the null at 21 DAI; however, CHR11 eggs/egg mass was only slightly reduced versus the null by 28 DAI. In contrast, CHR14 eggs/egg mass was like CHR11/CHR14, showing a 4-fold decrease compared with CHR11 and the null.


Assuntos
Gossypium , Locos de Características Quantitativas , Animais , Cromossomos Humanos Par 11 , Feminino , Fertilidade , Humanos , Doenças das Plantas
8.
Mol Genet Genomics ; 295(1): 67-79, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31473809

RESUMO

The use of genomic selection (GS) has stimulated a new way to utilize molecular markers in breeding for complex traits in the absence of phenotypic data. GS can potentially decrease breeding cycle by selecting the progeny in the early stages. The objective of this study was to experimentally evaluate the potential value of genomic selection in Upland cotton breeding. Six fiber quality traits were obtained in 3 years of replicated field trials in Starkville, MS. Genotyping-by-sequencing-based genotyping was performed using 550 recombinant inbred lines of the multi-parent advanced generation inter-cross population, and 6292 molecular markers were used for the GS analysis. Several methods were compared including genomic BLUP (GBLUP), ridge regression BLUP (rrBLUP), BayesB, Bayesian LASSO, and reproducing kernel hilbert spaces (RKHS). The average heritability (h2) ranged from 0.38 to 0.88 for all tested traits across the 3 years evaluated. BayesB predicted the highest accuracies among the five GS methods tested. The prediction ability (PA) and prediction accuracy (PACC) varied widely across 3 years for all tested traits and the highest PA and PACC were 0.65, and 0.69, respectively, in 2010 for fiber elongation. Marker density and training population size appeared to be very important factors for PA and PACC in GS. Results indicated that BayesB-based GS method could predict genomic estimated breeding value efficiently in Upland cotton fiber quality attributes and has great potential utility in breeding by reducing cost and time.


Assuntos
Genoma de Planta/genética , Gossypium/genética , Locos de Características Quantitativas/genética , Seleção Genética/genética , Teorema de Bayes , Cruzamento/métodos , Fibra de Algodão , Marcadores Genéticos/genética , Genômica/métodos , Modelos Genéticos , Fenótipo
9.
BMC Genomics ; 20(1): 112, 2019 Feb 06.
Artigo em Inglês | MEDLINE | ID: mdl-30727946

RESUMO

BACKGROUND: Improving cotton fiber length without reducing yield is one of the major goals of cotton breeding. However, genetic improvement of cotton fiber length by breeding has been a challenge due to the narrow genetic diversity of modern cotton cultivars and negative correlations between fiber quality and yield traits. A multi-parent advanced generation inter-cross (MAGIC) population developed through random mating provides an excellent genetic resource that allows quantitative trait loci (QTL) and causal genes to be identified. RESULTS: An Upland cotton MAGIC population, consisting of 550 recombinant inbred lines (RILs) derived from eleven different cultivars, was used to identify fiber length QTLs and potential genes that contribute to longer fibers. A genome wide association study (GWAS) identified a cluster of single nucleotide polymorphisms (SNPs) on chromosome (Chr.) D11 that is significantly associated with fiber length. Further evaluation of the Chr. D11 genomic region among lines of the MAGIC population detected that 90% of RILs have a D11 haplotype similar to the reference TM-1 genome (D11-ref), whereas 10% of RILs inherited an alternative haplotype from one of the parents (D11-alt). The average length of fibers of D11-alt RILs was significantly shorter compared to D11-ref RILs, suggesting that alleles in the D11-alt haplotype contributed to the inferior fiber quality. RNAseq analysis of the longest and shortest fiber length RILs from D11-ref and D11-alt populations identified 949 significantly differentially expressed genes (DEGs). Gene set enrichment analysis revealed that different functional categories of genes were over-represented during fiber elongation between the four selected RILs. We found 12 genes possessing non-synonymous SNPs (nsSNPs) significantly associated with the fiber length, and three that were highly significant and were clustered at D11:24-Mb, including D11G1928, D11G1929 and D11G1931. CONCLUSION: The results of this study provide insights into molecular aspects of genetic variation in fiber length and suggests candidate genes for genetic manipulation for cotton improvement.


Assuntos
Fibra de Algodão , Gossypium/genética , Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas , Transcriptoma , Alelos , Regulação da Expressão Gênica de Plantas , Genoma de Planta , Estudo de Associação Genômica Ampla , Gossypium/metabolismo , Melhoramento Vegetal , Proteínas de Plantas/genética
10.
Theor Appl Genet ; 132(5): 1425-1434, 2019 May.
Artigo em Inglês | MEDLINE | ID: mdl-30741320

RESUMO

KEY MESSAGE: MAGIC population sequencing and virus-induced gene silencing identify Gh_D02G0276 as a novel root-knot nematode resistance gene on chromosome 14 in Upland cotton. The southern root-knot nematode [RKN; Meloidogyne incognita (Kofoid & White)] remains the primary yield-limiting biotic stress to Upland cotton (Gossypium hirsutum L.) throughout the southeastern USA. While useful genetic markers have been developed for two major RKN resistance loci on chromosomes 11 (A11) and 14 (D02), these markers are not completely effective because the causative genes have not been identified. Here, we sequenced 550 recombinant inbred lines (RILs) from a multi-parent advanced generation intercross (MAGIC) population to identify five RILs that had informative recombinations near the D02-RKN resistance locus. The RKN resistance phenotypes of these five RILs narrowed the D02-RKN locus to a 30-kb region with four candidate genes. We conducted virus-induced gene silencing (VIGS) on each of these genes and found that Gh_D02G0276 was required for suppression of RKN egg production conferred by the Chr. D02 resistance gene. The resistant lines all possessed an allele of Gh_D02G0276 that showed non-synonymous mutations and was prematurely truncated. Furthermore, a Gh_D02G0276-specific marker for the resistance allele variant was able to identify RKN-resistant germplasm from a collection of 367 cotton accessions. The Gh_D02G0276 peptide shares similarity with domesticated hAT-like transposases with additional novel N- and C-terminal domains that resemble the target of known RKN effector molecules and a prokaryotic motif, respectively. The truncation in the resistance allele results in a loss of a plant nuclear gene-specific C-terminal motif, potentially rendering this domain antigenic due to its high homology with bacterial proteins. The conclusive identification of this RKN resistance gene opens new avenues for understanding plant resistance mechanisms to RKN as well as opportunities to develop more efficient marker-assisted selection in cotton breeding programs.


Assuntos
Genes de Plantas , Gossypium/genética , Nematoides/fisiologia , Animais , Biologia Computacional , Inativação Gênica , Variação Genética , Genótipo , Técnicas de Genotipagem , Gossypium/parasitologia
11.
Theor Appl Genet ; 132(4): 989-999, 2019 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-30506522

RESUMO

KEY MESSAGE: 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.


Assuntos
Fibra de Algodão/normas , Cruzamentos Genéticos , Loci Gênicos , Estudo de Associação Genômica Ampla , Genômica/métodos , Gossypium/genética , Sequenciamento Completo do Genoma , Cromossomos de Plantas/genética , Gossypium/anatomia & histologia , Endogamia , Anotação de Sequência Molecular , Fenótipo , Polimorfismo de Nucleotídeo Único/genética , Locos de Características Quantitativas/genética
12.
BMC Plant Biol ; 18(1): 186, 2018 Sep 10.
Artigo em Inglês | MEDLINE | ID: mdl-30200872

RESUMO

BACKGROUND: Weed management is critical to global crop production and is complicated by rapidly evolving herbicide resistance in weeds. New sources of herbicide resistance are needed for crop plants so that applied herbicides can be rotated or combined to thwart the evolution of resistant weeds. The diverse family of cytochrome P450 proteins has been suggested to be a source of detoxifying herbicide metabolism in both weed and crop plants, and greater understanding of these genes will offer avenues for crop improvement and novel weed management practices. RESULTS: Here, we report the identification of CYP749A16 (Gh_D10G1401) which is responsible for the natural tolerance exhibited by most cotton, Gossypium hirsutum L., cultivars to the herbicide trifloxysulfuron sodium (TFS, CGA 362622, commercial formulation Envoke). A 1-bp frameshift insertion in the third exon of CYP749A16 results in the loss of tolerance to TFS. The DNA marker designed from this insertion perfectly co-segregated with the phenotype in 2145 F2 progeny of a cross between the sensitive cultivar Paymaster HS26 and tolerant cultivar Stoneville 474, and in 550 recombinant inbred lines of a multi-parent advanced generation inter-cross population. Marker analysis of 382 additional cotton cultivars identified twelve cultivars containing the 1-bp frameshift insertion. The marker genotypes matched perfectly with phenotypes in 188 plants from the selected twelve cultivars. Virus-induced gene silencing of CYP749A16 generated sensitivity in the tolerant cotton cultivar Stoneville 474. CONCLUSIONS: CYP749A16 located on chromosome D10 is required for TFS herbicide tolerance in cotton. This finding should add to the repertoire of tools available to farmers and breeders for the advancement of agricultural productivity.


Assuntos
Sistema Enzimático do Citocromo P-450/genética , Gossypium/genética , Resistência a Herbicidas/genética , Herbicidas/toxicidade , Piridinas/toxicidade , Sulfonamidas/toxicidade , Mapeamento Cromossômico , Cromossomos de Plantas , Inativação Gênica , Gossypium/efeitos dos fármacos , Gossypium/enzimologia , Mutação
13.
BMC Genomics ; 19(1): 451, 2018 Jun 13.
Artigo em Inglês | MEDLINE | ID: mdl-29895260

RESUMO

BACKGROUND: Cottonseed is one of the most important raw materials for plant protein, oil and alternative biofuel for diesel engines. Understanding the complex genetic basis of cottonseed traits is requisite for achieving efficient genetic improvement of the traits. However, it is not yet clear about their genetic architecture in genomic level. GWAS has been an effective way to explore genetic basis of quantitative traits in human and many crops. This study aims to dissect genetic mechanism seven cottonseed traits by a GWAS for genetic improvement. RESULTS: A genome-wide association study (GWAS) based on a full gene model with gene effects as fixed and gene-environment interaction as random, was conducted for protein, oil and 5 fatty acids using 316 accessions and ~ 390 K SNPs. Totally, 124 significant quantitative trait SNPs (QTSs), consisting of 16, 21, 87 for protein, oil and fatty acids (palmitic, linoleic, oleic, myristic, stearic), respectively, were identified and the broad-sense heritability was estimated from 71.62 to 93.43%; no QTS-environment interaction was detected for the protein, the palmitic and the oleic contents; the protein content was predominantly controlled by epistatic effects accounting for 65.18% of the total variation, but the oil content and the fatty acids except the palmitic were mainly determined by gene main effects and no epistasis was detected for the myristic and the stearic. Prediction of superior pure line and hybrid revealed the potential of the QTSs in the improvement of cottonseed traits, and the hybrid could achieve higher or lower genetic values compared with pure lines. CONCLUSIONS: This study revealed complex genetic architecture of seven cottonseed traits at whole genome-wide by mixed linear model approach; the identified genetic variants and estimated genetic component effects of gene, gene-gene and gene-environment interaction provide cotton geneticist or breeders new knowledge on the genetic mechanism of the traits and the potential molecular breeding design strategy.


Assuntos
Gossypium/genética , Sementes/genética , Ácidos Graxos/análise , Genes de Plantas , Estudo de Associação Genômica Ampla , Genótipo , Gossypium/química , Melhoramento Vegetal , Proteínas de Plantas/genética , Característica Quantitativa Herdável , Sementes/química
14.
Water Air Soil Pollut ; 229(11): 1-13, 2018 Nov 03.
Artigo em Inglês | MEDLINE | ID: mdl-35153340

RESUMO

Assessment of surface water quality in the Mississippi Delta is essential to quantify the eutrophication of the Gulf of Mexico. This study estimated the characteristics and variations of surface water quality at three study sites in the Big Sunflower River Watershed (BSRW) within the Mississippi Delta using Kruskal-Wallis, Dunn, Mann-Kendall, and Pettitt tests. In general, contents of some water quality constituents such as nitrate-nitrogen (NO 3 - N) and total phosphorus (TP) in the BSRW varied from site to site each year, whereas variations of other constituents such as pH and dissolved oxygen (DO) each year were basically not significant. The highest median concentrations were found in spring for NO 3 - Nand total nitrogen (TN); in summer for specific conductance (SC), Na, and Cl; and in winter for DO. Mann-Kendall trend analysis revealed that there was an increasing annual trend at Leland but a decreasing annual trend at Merigold for NO 3 - Nconcentrations even though such changes were very small, whereas there was no annual trend for TP at any of the three study sites. Pettitt's test further identified that the NO 3 - N concentrations had an abrupt increase in February 2009 at the median value of 0.44 mg L-1 in Leland and an abrupt decrease in June 2012 at the median value of 3.65 mg L-1 in Merigold. A very good linear correlation exited between total dissolved solid (TDS) and magnesium (Mg) in the BSRW, which could be used to estimate TDS from Mg concentrations for this watershed when the data for TDS are absent.

15.
PLoS One ; 12(10): e0186240, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-29016665

RESUMO

Most wild and semi-wild species of the genus Gossypium are exhibit photoperiod-sensitive flowering. The wild germplasm cotton is a valuable source of genes for genetic improvement of modern cotton cultivars. A bi-parental cotton population segregating for photoperiodic flowering was developed by crossing a photoperiod insensitive irradiation mutant line with its pre-mutagenesis photoperiodic wild-type G. darwinii Watt genotype. Individuals from the F2 and F3 generations were grown with their parental lines and F1 hybrid progeny in the long day and short night summer condition (natural day-length) of Uzbekistan to evaluate photoperiod sensitivity, i.e., flowering-time during the seasons 2008-2009. Through genotyping the individuals of this bi-parental population segregating for flowering-time, linkage maps were constructed using 212 simple-sequence repeat (SSR) and three cleaved amplified polymorphic sequence (CAPS) markers. Six QTLs directly associated with flowering-time and photoperiodic flowering were discovered in the F2 population, whereas eight QTLs were identified in the F3 population. Two QTLs controlling photoperiodic flowering and duration of flowering were common in both populations. In silico annotations of the flanking DNA sequences of mapped SSRs from sequenced cotton (G. hirsutum L.) genome database has identified several potential 'candidate' genes that are known to be associated with regulation of flowering characteristics of plants. The outcome of this research will expand our understanding of the genetic and molecular mechanisms of photoperiodic flowering. Identified markers should be useful for marker-assisted selection in cotton breeding to improve early flowering characteristics.


Assuntos
Flores/genética , Estudos de Associação Genética , Gossypium/genética , Locos de Características Quantitativas/genética , Cruzamento , Flores/crescimento & desenvolvimento , Genoma de Planta , Genótipo , Gossypium/crescimento & desenvolvimento , Humanos , Repetições de Microssatélites/genética , Fotoperíodo , Reprodução , Têxteis , Uzbequistão
16.
Front Plant Sci ; 8: 1252, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-28791034

RESUMO

In crop research programs that implement transgene-based strategies for trait improvement it is necessary to distinguish between transgene homozygous and hemizygous individuals in segregating populations. Direct methods for determining transgene zygosity are technically challenging, expensive, and require specialized equipment. In this report, we describe a standard PCR-based protocol coupled with capillary electrophoresis that can identify transgene homozygous and hemizygous individuals in a segregating population without knowledge of transgene insertion site. PCR primers were designed to amplify conserved T-DNA segments of the 35S promoter, OCS terminator, and NPTII kanamycin resistance gene in the pHellsgate-8 RNAi construct for the Gossypium hirsutum phytochrome A1 gene. Using an optimized multiplexed reaction mixture and an amplification program of only 10 cycles we could discriminate between transgene homozygous and hemizygous cotton control DNA samples based on PCR product peak characteristics gathered by capillary electrophoresis. The protocol was refined by evaluating segregating transgenic progeny from nine BC1S1 populations derived from crosses between the transgenic cotton parent 'E-1-7-6' and other cotton cultivars. OCS PCR product peak height and peak area, normalized by amplification of the native cotton gene GhUBC1, revealed clear bimodal distributions of OCS product characteristics for each BC1S1 population indicating the presence of homozygous and hemizygous clusters which was further confirmed via K-means clustering. BC1S1 plants identified as homozygous or hemizygous were self-fertilized to produce BC1S2 progeny. For the homozygous class, 19/20 BC1S2 families confirmed the homozygous BC1S1 prediction while 21/21 BC1S2 families confirmed the hemizygous prediction of the original parent. This relatively simple protocol provides a reliable, rapid, and high-throughput way of evaluating segregating transgenic populations using methods and equipment common to crop molecular breeding labs.

17.
PLoS One ; 12(6): e0179381, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-28614407

RESUMO

Cotton fiber is an important commodity throughout the world. Fiber property determines fiber quality and commercial values. Previous studies showed that silencing phytochrome A1 gene (PHYA1) by RNA interference in Upland cotton (Gossypium hirsutum L. cv. Coker 312) had generated PHYA1 RNAi lines with simultaneous improvements in fiber quality (longer, stronger and finer fiber) and other key agronomic traits. Characterization of the altered molecular processes in these RNAi genotypes and its wild-type controls is a great interest to better understand the PHYA1 RNAi phenotypes. In this study, a total of 77 conserved miRNAs belonging to 61 families were examined in a PHYA1 RNAi line and its parental Coker 312 genotype by using multiplex sequencing. Of these miRNAs, seven (miR7503, miR7514, miR399c, miR399d, miR160, miR169b, and miR2950) were found to be differentially expressed in PHYA1 RNAi cotton. The target genes of these differentially expressed miRNAs were involved in the metabolism and signaling pathways of phytohormones, which included Gibberellin, Auxin and Abscisic Acid. The expression of several MYB transcription factors was also affected by miRNAs in RNAi cotton. In addition, 35 novel miRNAs (novel miR1-novel miR35) were identified in fibers for the first time in this study. Target genes of vast majority of these novel miRNAs were also predicted. Of these, nine novel miRNAs (novel-miR1, 2, 16, 19, 26, 27, 28, 31 and 32) were targeted to cytochrome P450-like TATA box binding protein (TBP). The qRT-PCR confirmed expression levels of several differentially regulated miRNAs. Expression patterns of four miRNAs-targets pairs were also examined via RNA deep sequencing. Together, the results imply that the regulation of miRNA expression might confer to the phenotype of the PHYA1 RNAi line(s) with improved fiber quality.


Assuntos
Fibra de Algodão , Regulação da Expressão Gênica de Plantas , Gossypium/genética , MicroRNAs/genética , Fitocromo A/genética , Interferência de RNA , Sistema Enzimático do Citocromo P-450/genética , Sistema Enzimático do Citocromo P-450/metabolismo , Perfilação da Expressão Gênica/métodos , Genoma de Planta/genética , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Plantas Geneticamente Modificadas , RNA de Plantas/genética , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Transdução de Sinais/genética , Proteína de Ligação a TATA-Box/genética , Proteína de Ligação a TATA-Box/metabolismo
18.
J Environ Qual ; 46(2): 339-347, 2017 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-28380557

RESUMO

The inability to incorporate broiler litter (BL) into permanent hayfields and pastures leads to nutrient accumulation near the soil surface and increases the potential transport of nutrients in runoff. This study was conducted on Marietta silt loam soil to determine the effect of flue gas desulfurization (FGD) gypsum and lignite on P, N, C, and microbial concentrations in runoff. Treatments were (i) control (unfertilized) and (ii) BL at 13.4 Mg ha alone or (iii) treated with either FGD gypsum or lignite applied at 20% (w/w) (2.68 Mg ha). Rainfall simulators were used to produce a 5.6 cm h storm event sufficient in duration to cause 15 min of continuous runoff. Repeated rains were applied at 3-d intervals to determine how long FGD gypsum and lignite are effective in reducing loss of litter-derived N, P, and C from soil. Application of BL increased N, P, and C concentrations in runoff as compared to the control. Addition of FGD gypsum reduced ( < 0.05) water-soluble P and dissolved organic C concentrations in runoff by 39 and 16%, respectively, as compared to BL alone. Lignite reduced runoff total N and NH-N concentrations by 38 and 70%, respectively, as compared to BL alone. Addition of FGD gypsum or lignite failed to significantly reduce microbial loads in runoff, although both treatments reduced microbial concentration by >20%. Thus, BL treated with FGD and lignite can be considered as cost-effective management practices in the mitigation of P, N, and C and possibly microbial concentration in runoff.


Assuntos
Esterco , Poluentes do Solo/análise , Microbiologia da Água , Animais , Galinhas , Fósforo , Chuva , Solo , Poluição da Água
19.
BMC Genomics ; 17(1): 903, 2016 11 09.
Artigo em Inglês | MEDLINE | ID: mdl-27829353

RESUMO

BACKGROUND: Cotton supplies a great majority of natural fiber for the global textile industry. The negative correlation between yield and fiber quality has hindered breeders' ability to improve these traits simultaneously. A multi-parent advanced generation inter-cross (MAGIC) population developed through random-mating of multiple diverse parents has the ability to break this negative correlation. Genotyping-by-sequencing (GBS) is a method that can rapidly identify and genotype a large number of single nucleotide polymorphisms (SNP). Genotyping a MAGIC population using GBS technologies will enable us to identify marker-trait associations with high resolution. RESULTS: An Upland cotton MAGIC population was developed through random-mating of 11 diverse cultivars for five generations. In this study, fiber quality data obtained from four environments and 6071 SNP markers generated via GBS and 223 microsatellite markers of 547 recombinant inbred lines (RILs) of the MAGIC population were used to conduct a genome wide association study (GWAS). By employing a mixed linear model, GWAS enabled us to identify markers significantly associated with fiber quantitative trait loci (QTL). We identified and validated one QTL cluster associated with four fiber quality traits [short fiber content (SFC), strength (STR), length (UHM) and uniformity (UI)] on chromosome A07. We further identified candidate genes related to fiber quality attributes in this region. Gene expression and amino acid substitution analysis suggested that a regeneration of bulb biogenesis 1 (GhRBB1_A07) gene is a candidate for superior fiber quality in Upland cotton. The DNA marker CFBid0004 designed from an 18 bp deletion in the coding sequence of GhRBB1_A07 in Acala Ultima is associated with the improved fiber quality in the MAGIC RILs and 105 additional commercial Upland cotton cultivars. CONCLUSION: Using GBS and a MAGIC population enabled more precise fiber QTL mapping in Upland cotton. The fiber QTL and associated markers identified in this study can be used to improve fiber quality through marker assisted selection or genomic selection in a cotton breeding program. Target manipulation of the GhRBB1_A07 gene through biotechnology or gene editing may potentially improve cotton fiber quality.


Assuntos
Fibra de Algodão , Genes de Plantas , Estudos de Associação Genética , Genética Populacional , Genoma de Planta , Estudo de Associação Genômica Ampla , Gossypium/genética , Cruzamento , Desequilíbrio de Ligação , Polimorfismo de Nucleotídeo Único , Característica Quantitativa Herdável
20.
BMC Genet ; 17(1): 141, 2016 10 24.
Artigo em Inglês | MEDLINE | ID: mdl-27776497

RESUMO

BACKGROUND: Among SNP markers that become increasingly valuable in molecular breeding of crop plants are the CAPS and dCAPS markers derived from the genes of interest. To date, the number of such gene-based markers is small in polyploid crop plants such as allotetraploid cotton that has A- and D-sub-genomes. The objective of this study was to develop and map new CAPS and dCAPS markers for cotton developmental-regulatory genes that are important in plant breeding programs. RESULTS: Gossypium hirsutum and G. barbadense, are the two cultivated allotetraploid cotton species. These have distinct fiber quality and other agronomic traits. Using comparative sequence analysis of characterized GSTs of the PHYA1, PHYB, and HY5 genes of G. hirsutum and G. barbadense one PHYA1-specific Mbo I/Dpn II CAPS, one PHYB-specific Alu I dCAPS, and one HY5-specific Hinf I dCAPS cotton markers were developed. These markers have successfully differentiated the two allotetraploid genomes (AD1 and AD2) when tested in parental genotypes of 'Texas Marker-1' ('TM-1'), 'Pima 3-79' and their F1 hybrids. The genetic mapping and chromosome substitution line-based deletion analyses revealed that PHYA1 gene is located in A-sub-genome chromosome 11, PHYB gene is in A-sub-genome chromosome 10, and HY5 gene is in D-sub-genome chromosome 24, on the reference 'TM-1' x 'Pima 3-79' RIL genetic map. Further, it was found that genetic linkage map regions containing phytochrome and HY5-specific markers were associated with major fiber quality and flowering time traits in previously published QTL mapping studies. CONCLUSION: This study detailed the genome mapping of three cotton phytochrome genes with newly developed CAPS and dCAPS markers. The proximity of these loci to fiber quality and other cotton QTL was demonstrated in two A-subgenome and one D-subgenome chromosomes. These candidate gene markers will be valuable for marker-assisted selection (MAS) programs to rapidly introgress G. barbadense phytochromes and/or HY5 gene (s) into G. hirsutum cotton genotypes or vice versa.


Assuntos
Mapeamento Cromossômico , Genes de Plantas , Genoma de Planta , Genômica , Gossypium/genética , Locos de Características Quantitativas , Ligação Genética , Marcadores Genéticos , Genômica/métodos , Gossypium/metabolismo , Fitocromo , Característica Quantitativa Herdável
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