Johnie N. Jenkins

An RFLP linkage map of Upland cotton, Gossypium hirsutum L.

Abstract Ninety-six F2.F3 bulked sampled plots of Upland cotton, Gossypium hirsutum L., from the cross of HS46×MARCABUCAG8US-1-88, were analyzed with 129 probe/enzyme combinations resulting in 138 RFLP loci. Of the 84 loci that segregated as co-dominant, 76 of these fit a normal 1 :  2 : 1 ratio (non-significant chi square at P=0.05). Of the 54 loci that segregated as dominant genotypes, 50 of these fit a normal 3: 1 ratio (non-significant chi square at P=0.05). These 138 loci were analyzed with the MAPMAKER∖ EXP program to determine linkage relationships among them. There were 120 loci arranged into 31 linkage groups. These covered 865 cM, or an estimated 18.6% of the cotton genome. The linkage groups ranged from two to ten loci each and ranged in size from 0.5 to 107 cM. Eighteen loci were not linked.

A High-Density Simple Sequence Repeat and Single Nucleotide Polymorphism Genetic Map of the Tetraploid Cotton Genome

Genetic linkage maps play fundamental roles in understanding genome structure, explaining genome formation events during evolution, and discovering the genetic bases of important traits. A high-density cotton (Gossypium spp.) genetic map was developed using representative sets of simple sequence repeat (SSR) and the first public set of single nucleotide polymorphism (SNP) markers to genotype 186 recombinant inbred lines (RILs) derived from an interspecific cross between Gossypium hirsutum L. (TM-1) and G. barbadense L. (3-79). The genetic map comprised 2072 loci (1825 SSRs and 247 SNPs) and covered 3380 centiMorgan (cM) of the cotton genome (AD) with an average marker interval of 1.63 cM. The allotetraploid cotton genome produced equivalent recombination frequencies in its two subgenomes (At and Dt). Of the 2072 loci, 1138 (54.9%) were mapped to 13 At-subgenome chromosomes, covering 1726.8 cM (51.1%), and 934 (45.1%) mapped to 13 Dt-subgenome chromosomes, covering 1653.1 cM (48.9%). The genetically smallest homeologous chromosome pair was Chr. 04 (A04) and 22 (D04), and the largest was Chr. 05 (A05) and 19 (D05). Duplicate loci between and within homeologous chromosomes were identified that facilitate investigations of chromosome translocations. The map augments evidence of reciprocal rearrangement between ancestral forms of Chr. 02 and 03 versus segmental homeologs 14 and 17 as centromeric regions show homeologous between Chr. 02 (A02) and 17 (D02), as well as between Chr. 03 (A03) and 14 (D03). This research represents an important foundation for studies on polyploid cottons, including germplasm characterization, gene discovery, and genome sequence assembly.

Simple sequence repeats as useful resources to study transcribed genes of cotton

Microsatellites or Simple Sequence Repeats(SSRs) are informative molecular genetic markers in many crop species. SSRs are PCR-based, highly polymorphic, abundant, widely distributed throughout the genome and inherited in a co-dominant manner in most cases. Here we describe the presence of SSRs in cDNAs of cotton. Thirty one SSR primer pairs of 220 (∼14%) tested led to PCR amplification of discrete fragments using cotton leaf cDNA as template. Sequence analysis showed 25% of 24randomly selected cDNA clones amplified with different SSR primer pairs contained repeat motifs. We further showed that sequences from the SSR-containing cDNAs were conserved across G. barbadense and G. hirsutum, revealing the importance of the SSR markers for comparative mapping of transcribed genes. Data mining for plant SSR-ESTs from the publicly available databases identified SSRs motifs in many plant species,including cotton, in a range of 1.1 to4.8% of the submitted ESTs for a given species.

Resistance of Plants to Insects

Publisher Summary This chapter discusses the resistance of plants to insects. Resistance is the ability of a certain variety to produce a larger yield of good quality than other varieties at the same initial level of infestation and under similar environmental conditions. Three basic components or mechanisms are involved in plant resistance. First, plants may be nonpreferred for oviposition, shelter, or food, primarily, because of the lack of or presence of chemical or physical factors. Second, resistant plants may affect the biology of the insect adversely that is called antibiosis. Third, resistant plants may be tolerant, surviving under levels of infestation that would kill or severely injure susceptible plants. Several problems may occur at various stages in the development of any host plant resistance program. Some of these problems include: proper finance, entomological problems, and problems in technique development. Resistance is most often found in off types or exotic wild species, and considerable crossing and selection is required to move the resistant genes into a desirable agronomic background. The greatest use of resistant varieties would undoubtedly be as one component part of pest management system.

Evaluation of genetic variances, heritabilities, and correlations for yield and fiber traits among cotton F2 hybrid populations

SummaryF2 hybrid cultivars continue to occupy a small portion of the cotton (Gossypium hirsutum L.) production are in the United States, but occupy a larger proportion of the production area in some other countries. Sixty-four F2 hybrids resulting from crosses of four commercial cultivars and 16 pest-resistant germplasm lines were evaluated for five fiber and four yield traits in four environments at Mississippi State, MS. An additive-dominance genetic model was employed for these traits. The minimum norm quadratic unbiased estimation (MINQUE) method was used with a mixed model approach for estimating genetic variance and covariance components and for predicting genetic correlations. This study investigated genetic variances, heritabilities, and genetic and phenotypic correlations between agronomic and fiber traits among these 64 F2 hybrid populations and discussed the usefulness of these populations for use as hybrids or for selections for pure lines.Dominance variance accounted for the major proportion of the phenotypic variances for lint yield, lint percentage, and boll size indicating that hybrids should have an advantage for these traits compared to pure lines. A low proportion of additive variance for fiber traits and the significant additive x environment variance components indicated a lack of substantial useful additive genetic variability for fiber traits. This suggests that selections for pure lines within these F2 populations would have limited success in improving fiber traits. Genetic and phenotypic correlation coefficients were of comparable magnitude for most pairs of characters. Fiber strength showed a positive additive genetic correlation with boll weight. Dominance genetic correlations of fiber strength with elongation and 2.5% span length were also significant and positive; however, the additive genetic correlation of length and strength was zero.

Effects of Chromosome-Specific Introgression in Upland Cotton on Fiber and Agronomic Traits

Interspecific chromosome substitution is among the most powerful means of introgression and steps toward quantitative trait locus (QTL) identification. By reducing the genetic “noise” from other chromosomes, it greatly empowers the detection of genetic effects by specific chromosomes on quantitative traits. Here, we report on such results for 14 cotton lines (CS-B) with specific chromosomes or chromosome arms from G. barbadense L. substituted into G. hirsutum and chromosome-specific F2 families. Boll size, lint percentage, micronaire, 2.5% span length, elongation, strength, and yield were measured by replicated field experiments in five diverse environments and analyzed under an additive–dominance (AD) genetic model with genotype and environment interaction. Additive effects were significant for all traits and dominance effects were significant for all traits except 2.5% span length. CS-B25 had additive effects increasing fiber strength and fiber length and decreasing micronaire. CS-B16 and CS-B18 had additive effects related to reduced yields. The results point toward specific chromosomes of G. barbadense 3-79 as the probable locations of the genes that significantly affect quantitative traits of importance. Our results provided a scope to analyze individual chromosomes of the genome in homozygous and heterozygous conditions and thus detected novel effects of alleles controlling important QTL.

Differential expression of a lipid transfer protein gene in cotton fiber.

A full-length cDNA clone, GH3, has been isolated from a cotton fiber cDNA library using a differential screening method. The nucleotide and derived amino acid sequence data show that GH3 encodes a lipid transfer protein (LTP) of 120 amino acids. The presence of a transmembrane signal peptide at the N-terminal of the protein would suggest its possible outer cellular location in fiber cells. Northern analysis indicates that the GH3 gene is developmentally regulated.

Development of a 63K SNP Array for Cotton and High-Density Mapping of Intraspecific and Interspecific Populations of Gossypium spp.

High-throughput genotyping arrays provide a standardized resource for plant breeding communities that are useful for a breadth of applications including high-density genetic mapping, genome-wide association studies (GWAS), genomic selection (GS), complex trait dissection, and studying patterns of genomic diversity among cultivars and wild accessions. We have developed the CottonSNP63K, an Illumina Infinium array containing assays for 45,104 putative intraspecific single nucleotide polymorphism (SNP) markers for use within the cultivated cotton species Gossypium hirsutum L. and 17,954 putative interspecific SNP markers for use with crosses of other cotton species with G. hirsutum. The SNPs on the array were developed from 13 different discovery sets that represent a diverse range of G. hirsutum germplasm and five other species: G. barbadense L., G. tomentosum Nuttal × Seemann, G. mustelinum Miers × Watt, G. armourianum Kearny, and G. longicalyx J.B. Hutchinson and Lee. The array was validated with 1,156 samples to generate cluster positions to facilitate automated analysis of 38,822 polymorphic markers. Two high-density genetic maps containing a total of 22,829 SNPs were generated for two F2 mapping populations, one intraspecific and one interspecific, and 3,533 SNP markers were co-occurring in both maps. The produced intraspecific genetic map is the first saturated map that associates into 26 linkage groups corresponding to the number of cotton chromosomes for a cross between two G. hirsutum lines. The linkage maps were shown to have high levels of collinearity to the JGI G. raimondii Ulbrich reference genome sequence. The CottonSNP63K array, cluster file and associated marker sequences constitute a major new resource for the global cotton research community.

Analysis of promoter activity of cotton lipid transfer protein gene LTP6 in transgenic tobacco plants

A cotton (Gossypium hirsutum) genomic clone (1.7-kb DNA insert) harboring the lipid transfer gene Ltp6 specifically expressed in fiber cells had been previously isolated and characterized. By using PCR amplification, the 447 bp Ltp6 promoter and a series of 5% deletions of the promoter were generated and cloned into a pBI101 plasmid upstream of the GUS (b-glucuronidase) reporter gene. These constructs were introduced into Agrobacterium tumefaciens LBA4404, and leaf disks of tobacco (Nicotiana tabacum L.) were transformed with A. tumefaciens LBA4404 carrying various promoter-GUS pBI101 plasmids. Histochemical analyses of the transgenic tobacco seedlings indicated that the Ltp6 promoter (from nt 447 to 1, undeleted) directed GUS expression only in trichomes (hair cells). Fluorometric GUS assays showed that the promoter activity of the undeleted Ltp6 promoter was at least 1000 times weaker than that of the 35S promoter of cauliflower mosaic virus (CaMV). Sequential deletions of the promoter gradually decreased the expression level of the GUS gene. No GUS activity was observed when the 5% deletion of the Ltp6 promoter reached to nt 86, which removed the putative CAAT and TATA promoter elements.

Analysis of a precision agriculture approach to cotton production

The hope of precision agriculture is that through more precise timing and usage of seed, agricultural chemicals and irrigation water that higher economic yields can occur while enhancing the economic production of field crops and protecting the environment. The analyses performed in this manuscript demonstrate proof of concept of how precision agriculture coupled with crop simulation models and geographic information systems technology can be used in the cotton production system in the Mid South to optimize yields while minimizing water and nitrogen inputs. The Hood Farm Levingston Field, located in Bolivar County, Mississippi, next to the Mississippi River, was chosen as the test sight to obtain a one hectare soil physical property grid over the entire 201 ha field. The 1997 yield was used as a comparison for the analysis. Actual cultural practices for 1997 were used as input to the model. After the 201 simulations were made using the expert system to optimize for water and nitrogen on a one hectare basis, the model predicted that an increase of 322 kg/ha could be obtained by using only an average increase of 2.6 cm of water/ha and an average decrease of 35 kg N/ha.