Genetic analyses of complex traits in wheat (Triticum aestivum L.) are facilitated by the availability of unique genetic tools such as chromosome substitution lines and recombinant inbred chromosome lines (RICLs) which allow the effects of genes on single chromosomes to be studied individually. Chromosome 3A of ‘Wichita’ is known to contain alleles at quantitative trait loci (QTLs) that influence variation in grain yield and agronomic performance traits relative to alleles of ‘Cheyenne’. To determine the number, location, and environmental interactions of genes related to agronomic performance on chromosome 3A, QTL and QTL × environment analyses of 98 RICLs‐3A were conducted in seven locations across Nebraska from 1999 through 2001. QTLs were detected for seven of eight agronomic traits measured and generally localized to three regions of chromosome 3A. QTL × environment interactions were detected for some QTLs and these interactions were caused by changes in magnitude and crossover interactions. Major QTLs for kernels per square meter and grain yield were associated within a 5‐centimorgan (cM) interval and appeared to represent a single QTL with pleiotropic effects. This particular QTL displayed environmental interactions caused by changes in magnitude, wherein the positive effect of the Wichita QTL allele was larger in higher yielding environments.

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.

BackgroundCotton (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.ResultsFrom 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.ConclusionThis 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.

Biomass production represents a fundamental biological process of both ecological and agricultural significance. The genetic basis of biomass production is unknown but asssumed to be complex. We developed a full sib, F1 mapping population of autotetraploid Medicago sativa (alfalfa) derived from an intersubspecific cross that was known to produce heterosis for biomass production. We evaluated the population for biomass production over several years at three locations (Ames, IA, Nashua, IA, and Ithaca, NY) and concurrently developed a genetic linkage map using restriction fragment length polymorphism (RFLP) and simple sequence repeat (SSR) molecular markers. Transgressive segregants, many of which exhibited high levels of heterosis, were identified in each environment. Despite the complexities of mapping within autotetraploid populations, single‐marker analysis of variance identified 41 marker alleles, many on linkage groups 5 and 7, associated with biomass production in at least one of the sampling periods. Seven alleles were associated with biomass production in more than one of the sampling periods. Favorable alleles were contributed by both parents, one of which is from the M. sativa subsp. falcata germplasm. Thus, increased biomass production alleles can be gleaned from unadapted germplasm. Further, the positive quantitative trait locus (QTL) alleles from the parents are partially complementary, suggesting these loci may play a role in biomass production heterosis.

Plant breeding programs involving a wide range of crop plants routinely practice selection (directly or indirectly) for genotypes that display stability for a given trait or set of traits across testing environments through the genotype evaluation process. Genotype stability for trait performance is a direct measure of the presence and effect of genotype × environment interactions, which result from the differential performance of a genotype or cultivar across environments. The genotype evaluation process also requires selection of the proper field trial locations that best represent the target environments the breeding program is directed toward. In this study, we assessed the extent to which genotype × environment interactions affected agronomic performance (lint yield, gin turnout) and fiber quality (fiber length, fiber strength, uniformity index, micronaire, fiber elongation) in a series of cotton (Gossypium hirsutum) performance trials in 12 location-year environments in South Carolina. Genotype × environment interactions affecting lint yield were larger in higher yielding environments, while interactions for fiber strength were greater for genotypes with lower mean fiber strength values. Two regions within the South Carolina cotton production areas were identified as proper testing locations for lint yield performance, while testing for fiber strength can be accomplished in any location within the statewide cotton production areas.Abbreviations: AMMI: additive main effects and multiplicative interactions model; ANOVA: analysis of variance; G × E: genotype × environment interaction; IPCA: interaction principal component axis

The cultivated Gossypium spp. (cotton) represents the single most important, natural fiber crop in the world. In addition to its fiber, the oil and protein portion of the cottonseed also represents significant economic value. To protect the worldwide economic value of cotton fiber and cotton byproducts, coordinated efforts to collect and maintain cotton genetic resources have increased over the last 100 yr. The classified genetic resources of cotton are extensive and include five tetraploid species in the primary gene pool, 20 diploid species in the secondary gene pool, and 25 diploid species in the tertiary gene pool. This report provides information on the status and contents of eight major cotton germplasm collections present across the world. Based on the findings of this report, a number of classified Gossypium species are not maintained in these collections, and several are underrepresented and vulnerable to extinction. This report presents several critical challenges and opportunities facing international efforts to enhance and preserve the world's Gossypium genetic resources. Multinational communication and collaboration are essential to protect, secure, and evaluate the global cotton germplasm resources. Without global, collaborative efforts, the rarest and most unique cotton germplasm resources are vulnerable to extinction.

Besides nodulating the original trap host, the isolates formed nitrogen-fixing symbioses with Phaseolus vulgaris. Only half of the isolates nodulated alfalfa (Medicago sativa), but these did not form nitrogen-fixing symbioses. Rhizobium tropici also formed nitrogen-fixing symbioses with Medicago ruthenica. A total of 56 distinctive multilocus electrophoretic types (ETs) were identified among 94 of the 106 isolates which were analysed for variation in electrophoretic mobility of 12 enzyme loci. One isolate (USDA 1920) possessed a unique El, while the ETs of the other isolates formed two weakly divergent subgroups approximately equal in size. It was concluded from small subunit rRNA gene sequences of eight isolates of Medicago ruthenica that they belonged to the genus Rhizobium and not to the genus Sinorhizobium which is more commonly associated with Medicago. Genomic similarity, determined from DNA hybridization analysis, between USDA 1920 and the strain representing the remaining isolates (USDA 1844) was lower than 20%. Based upon these observations it was concluded that at least three genomic species of rhizobia form nitrogen-f ixing symbioses with Medicago ruthenica. One of these genomic species is R. tropici, another is represented by the single isolate USDA 1920 and the name Rhizobium mongolense is proposed for the third genomic species represented by USDA 1844.

One of the most significant, long-term public U.S. Upland cotton {Gossypium hirsutum L.) germplasm enhancement programs is known as the Pee Dee germplasm program. The unique, genetic foundation of the Pee Dee germplasm was created using germplasm from Upland, Sea Island {Gossypium barbadense L.), and primitive diploid cottons. Since the program's inception in 1935, the Pee Dee germplasm program has released >80 improved germplasm lines and cultivars. In this study, the agronomic and fiber quality performance of Pee Dee germplasm was evaluated across southeastern U.S. environments to estimate genetic improvement within the Pee Dee germplasm program. Results suggest that the Pee Dee germplasm enhancement program has (i) maintained usable genetic variation and (ii) maintained high fiber quality potential while concomitantly improving agronomic performance. Although the results highlight the need to continue improving lint percent, lint yield, and bolls m'^, there is also evidence to suggest that Pee Dee germplasm can continue being utilized to develop the next generation of high-fiberquality and high-yielding cotton cultivars.