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Background The southern root-knot nematode (Meloidogyne incognita; RKN) is one of the most important economic pests of Upland cotton (Gossypium hirsutum L.). Host plant resistance, the ability of a plant to suppress nematode reproduction, is the most economical, practical, and environmentally sound method to provide protection against this subterranean pest. The resistant line Auburn 623RNR and a number of elite breeding lines derived from it remain the most important source of root-knot nematode (RKN) resistance. Prior genetic analysis has identified two epistatically interacting RKN resistance QTLs, qMi-C11 and qMi-C14, affecting gall formation and RKN reproduction, respectively. Results We developed a genetic population segregating only for the qMi-C14 locus and evaluated the genetic effects of this QTL on RKN resistance in the absence of the qMi-C11 locus. The qMi-C14 locus had a LOD score of 12 and accounted for 24.5 % of total phenotypic variation for egg production. In addition to not being significantly associated with gall formation, this locus had a lower main effect on RKN reproduction than found in our previous study, which lends further support to evidence of epistasis with qMi-C11 in imparting RKN resistance in the Auburn 623RNR source. The locus qMi-C14 was fine-mapped with the addition of 16 newly developed markers. By using the reference genome sequence of G. raimondii, we identified 20 candidate genes encoding disease resistance protein homologs in the newly defined 2.3 Mb region flanked by two SSR markers. Resequencing of an RKN resistant and susceptible G. hirsutum germplasm revealed non-synonymous mutations in only four of the coding regions of candidate genes, and these four genes are consequently of high interest. Conclusions Our mapping results validated the effects of the qMi-C14 resistance locus, delimiting the QTL to a smaller region, and identified tightly linked SSR markers to improve the efficiency of marker-assisted selection. The candidate genes identified warrant functional studies that will help in identifying and characterizing the actual qMi-C14 defense gene(s) against root-knot nematodes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2954-1) contains supplementary material, which is available to authorized users.

A major fi ber strength quantitative trait locus (QTL) has been identifi ed on chromosome 24 in the Chinese germplasm line ‘Suyuan 7235’; however, the effects of this QTL have not been tested in different genetic backgrounds. In this study, we confi rmed the effects of this QTL by crossing Suyuan 7235 with two U.S. germplasm lines with different fi ber strength. This QTL was consistently expressed over generations and years in both populations. The Suyuan 7235 allele explained up to 40% of the total phenotypic variation and accounted for an increase of up to 22.8 kN m kg –1 . The effects on fi ber strength appear to be greater in Suyuan 7235 × ‘Sealand 883’ (Pop-883) than in Suyuan 7235 × ‘Sealand 542’ (Pop-542) despite the Sealand 883 parent having stronger fi ber than the Sealand 542 parent. Deoxyribonucleic acid fi ngerprinting on a collection of elite cotton (Gossypium hirsutum L.) lines indicated that this QTL is not present in a survey of elite U.S. public germplasm. These results indicate that this fi ber strength QTL could signifi cantly improve the economic value of Upland cottons in the United States. The identifi cation of 27 novel markers tightly linked in this region adds additional tools to allow this QTL to be more effi ciently deployed in breeding cultivars with improved fi ber strength.

Genotype × environment (G × E) interactions and trait correlations signifi cantly impact efforts to develop high-yield, high-quality, and environmentally stable Upland cotton (Gossypium hirsutum L.) cultivars. Knowledge of both can and should be used to design optimal breeding programs and effective selection criteria. In this study, we examined the G × E interactions and trait correlations present in the 70-yr Pee Dee cotton germplasm enhancement program. Since beginning in 1935, the Pee Dee program has employed a variety of unique germplasm and breeding methods to release >80 improved germplasm lines and cultivars. Results suggest that signifi cant G × E interactions exist for several agronomic and fi ber quality performance traits that are mostly due to changes in magnitude. Negative genotypic correlations still persist between lint percent/lint yield and fi ber length/fi ber strength. However, apparently the breeding methods and selection criteria used over 70 yr have lessened the negative relationship between agronomic performance and fi ber quality over time to some degree. The results provide cotton breeders a resource to select specifi c Pee Dee germplasm lines for increased environmental stability. Cotton breeders can also use the information herein to select speci fi c Pee Dee germplasm lines that represent rare recombination events that combine high yield and fi ber quality potential.

GA 120R1B3 (Reg. No. GP-931, PI 660980) is a noncommercial breeding line of cotton (Gossypium hirsutum L.) jointly released by the USDA-ARS and the Agricultural Experiment Station at the University of Georgia in 2010. GA 120R1B3 was created using a single-seed descent method in a backcrossing program to combine the resistance to Meloidogyne incognita (southern root-knot nematode) from M-120 RNR with the high-yielding, high fiber-quality characteristics of PD 94042. Two greenhouse evaluations of nematode reproduction were conducted in 2007. Field evaluations for yield and fiber quality were conducted from 2007 to 2009 and included three tests in fields infested with M. incognita and four tests in fields without M. incognita. GA 120R1B3 has a high level of resistance to M. incognita that is equivalent to that found in M-120 RNR, but GA 120R1B3 has significantly better lint percentage and fiber quality than M-120 RNR. GA 120R1B3 has a yield and fiber quality generally comparable to commercial cultivars and a lint percentage that was often greater than that of the commercial standards. GA 120R1B3 had good yield and excellent fiber quality in both the presence and absence of M. incognita.

Inanearlieradvanced-backcrossquantitative� traitlocus�(QTL)�analysisofaninterspecificGos- sypium hirsutumL.��Gossypium barbadenseL.� population,�28�fiberlengthQTLswereidentified� includingqFL-chr1� onchromosome� 1� ofthe� A-subgenome.�TheG. barbadensealleleatthis� QTLcontributedtolongerfibersandexplained� upto�24%�ofthephenotypicvariance.�Tosub- stantiatetheassociationofthisgenomicregion� withfiberlength,� threeBC 3 F 2 � plantsheterozy- gousforthegeneticmarkersthatdelineatethe� qFL-chr1�QTLwereselectedtoconstructthree� independentpopulationsofnear-isogenicintro- gressionlines� (NIILs).� TheefficacyofqFL-chr1� wasevaluatedamong� 140� NIILsgrownin� 2� yr.� TheresultssupportthepositiveeffectofqFL- chr1� onfiberlength.� AsingleNIIL,� R01-40-08,� hadabout� 94.3%� ofrecurrentgenomecom- positionandsignificantlylongerfiberthanthe� recurrentparentwhengrowninNanjing,�China.� Therefore,�inadditiontoconfirmingtheefficacy� ofqFL-chr1� toenhancefiberlength,� thiswork� providesavaluablegeneticresourceforthe� improvementofcotton.

Seventeen backcross-self families from crosses between two Gossypium hirsutum recurrent parent lines (CA3084, CA3093) and G. tomentosum were used to identify quantitative trait loci (QTLs) controlling fiber quality traits. A total of 28 QTLs for fiber quality traits were identified (P0.001), including four for fiber elongation, eight for fiber fineness, four for fiber length, four for fiber strength, six for fiber uniformity, one for boll weight, and one for boll number. Three statistically significant marker-trait associations for lint yield were found in a single environment, but need further validation. Two-way analysis of variance revealed one locus with significant genotype × family interaction (P0.001) for fiber strength and a second locus with significant genotype × environment interaction (P0.001) in the CA3084 background, and two loci with significant genotype × background interaction (P0.001) for the 28 common markers segregating in both of the two recurrent backgrounds. Co-location of many QTLs for fiber quality traits partially explained correlations among these traits. Some G. tomentosum alleles were associated with multiple favorable effects, offering the possibility of rapid genetic gain by introgression. Many G. tomentosum alleles were recalcitrant to homozygosity, suggesting that they might be most effectively deployed in hybrid cottons. DNA markers linked to G. tomentosum QTLs identified in the present study promise to assist breeders in transferring and maintaining valuable traits from this exotic source during Upland cotton cultivar development. This study also adds further evidence to prior studies indicating that the majority of genetic variation associated with fiber quality in tetraploid cotton traces to the D-subgenome from a diploid ancestor that does not produce spinnable fiber.

One of the most signifi cant, 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 fi ber 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 fi ber quality potential while concomitantly improving agronomic performance. Although the results highlight the need to continue improving lint percent, lint yield, and bolls m −2 , there is also evidence to suggest that Pee Dee germplasm can continue being utilized to develop the next generation of high-fi berquality and high-yielding cotton cultivars.

The upland cotton (Gossypium hirsutum L.) germplasm line CRB 252 (Reg. No GP-925, PI 658596) was developed, evaluated, and jointly released in 2009 by the USDA-ARS, the Louisiana Agricultural Experiment Station, the Georgia Agricultural Experiment Station, and Cotton Incorporated. The purpose of the release was to provide a broadly adapted, high fi ber-quality resource for facilitating fi ber improvement efforts across the U.S. Cotton Belt. CRB 252 originated from the cross 'Suregrow 248'/'Phytogen 72'//'Stoneville 474'/'Acala Maxxa', followed by individual plant selection in the F2 and F3 generations at the low-desert location of Maricopa, AZ and F3.5 progeny selection at fi ve locations distributed across the Cotton Belt. Evaluation of CRB 252 occurred in 13 location-year environments at Florence, SC; Blackville, SC; Tifton, GA; Plains, GA; Alexandria, LA; Maricopa, AZ; and Shafter, CA in 2007 and 2008. CRB 252 displayed fi ber length and micronaire values superior to those of the high fi ber-quality check cultivars Phytogen 72 and FM 958. The fi ber strength and short-fi ber content of CRB 252 was superior to those of FM 958. Lint yield of CRB 252 was superior to that of Phytogen 72 and did not differ from FM 958. CRB 252 is an excellent source of quality fi ber, with acceptable yield potential that appears to be stable across production environments.

The identification and utilization of a high-level of host plant resistance is the most effective and economical approach to control root-knot nematode (Meloidogyne incognita). In an earlier study, we identified a major quantitative trait locus (QTL) for resistance to root-knot nematode in the M-120 RNR Upland cotton line (Gossypium hirsutum L.) of the Auburn 623 RNR source. The QTL is located in a 12.9-cM interval flanked by the two SSR markers CIR069 and CIR316 on the distal segment of chromosome 11. To construct a fine map around the target region, a bulked segregation analysis was performed using two DNA pools consisting of five individuals, with each being homozygous for the two parental alleles. From a survey of 1,152 AFLP primer combinations, 9 AFLP markers closely linked to the target region were identified. By screening an additional 1,221 F(2) individuals developed from the initial mapping population, the Mi-C11 locus was delimited to a 3.6-cM interval flanked by the SSR marker CIR069 and the AFLP marker E14M27-375. These results further elucidate the genetic fine structure of the Mi-C11 locus and provide the basis for map-based isolation of the nematode resistance gene in M-120 RNR.

Revealing the genetic underpinnings of cotton productivity will require understanding both the prehistoric evolution of spinnable fibers, and the results of independent domestication processes in both the Old and New Worlds. Progress toward a reference sequence for the smallest Gossypium genome is a logical stepping-stone toward revealing diversity in the remaining seven genomes (A, B, C, E, F, G, K) that permitted Gossypium species to adapt to a wide range of ecosystems in warmer arid regions of the world, and toward identifying the emergent properties that account for the superior productivity and quality of tetraploid cottons. The greatest challenge facing the cotton community is not genome sequencing per se but the conversion of sequence to knowledge.

The National Plant Germplasm System (NPGS) is a cooperative effort among State, Federal and Private organizations aimed at preserving one of agriculture’s greatest assets: plant genetic diversity. The NPGS serves the scientific community by collecting, storing, and distributing germplasm as well as maintaining a searchable database of trait descriptors. Serving the NPGS, a Crop Germplasm Committee (CGC) is elected for each crop and is comprised of a group of scientists concerned with development, maintenance, characterization, and utilization of germplasm collections. Each CGC serves in an advisory role and provides a status report every seven years to determine scientific efforts, adequacy of germplasm base representation, and progress in breeding through utilization of germplasm. In addition, each committee can call attention to areas of concerns regarding facilities and staffing associated with the maintenance, collection, and taxonomic activities for a specific crop within the system. The following report was developed by the CGC for cotton and provides a record of collections, activities, concerns, crop vulnerabilities, and recommendations associated with the cotton collection for the period 1997–2005. Information provided within this document is a much expanded and detailed description of a report provided to the NPGS and includes the most exhaustive citation of germplasm depositions and research activity descriptions available anywhere in the USA for this time period. This documentation will be a valuable resource to breeders, geneticists, and taxonomists with an interest in this important food and fiber crop.

Quantitative trait loci (QTLs) for yield and drought related physiological traits, osmotic potential (OP), carbon isotope ratio (d 13 C, an indica- tor of water use efficiency), and leaf chlorophyll content (Chl), were exchanged via marker-assisted selection (MAS) between elite cultivars of the two cotton species Gossypium barbadense cv. F-177 and G. hirsutum cv. Siv'on. The resulting near isogenic lines (NILs) were examined in two field trials, each with two irrigation regimes, in order to (1) evaluate the potential to improve cotton drought resistance by MAS and (2) test the role of physiological traits in plant productivity. NILs introgressed with QTLs for high yield rarely exhibited an advantage in yield relative to the recipient parent, whereas a considerable number of NILs exhibited the expected phenotype in terms of lower OP (5 out of 9), higher d 13 C (4 out of 6) or high Chl (2 out of 3). Several NILs exhibited considerable modifications in non-targeted traits including leaf morphology, stomatal conductance and specific leaf weight (SLW). In G. barbadense genotypes, yield was correlated negatively with d 13 C and OP and positively with stomatal conductance, SLW and Chl, whereas in G. hirsutum yield was negatively correlated with d 13 C, SLW and Chl. This dissimilarity suggests that each of the respective species has evolved different mechanisms underlying plant productivity. We conclude that the improvement of drought related traits in cotton NILs may lead to improved drought resistance via MAS, but that conventional breeding may be necessary to combine the introduced QTL(s) with high yield potential.

Quantitative variation for leaf trichome number is observed within and among Gossypium species, varying from glabrous to densely pubescent phenotypes. Moreover, economically important cotton lint fibers are modified trichomes. Earlier studies have mapped quantitative trait loci (QTLs) affecting leaf pubescence in Gossypium using allotetraploids. In this study, we mapped genes responsible for leaf trichome density in a diploid A genome cross. We were able to map 3 QTLs affecting leaf pubescence based on trichome counts obtained from young leaves (YL) and mature leaves (ML). When the F(2) progeny were classified as pubescent versus glabrous, their ratio did not deviate significantly from a 3:1 model, suggesting that glabrousness is inherited in a simple Mendelian fashion. The glabrous mutation mapped to linkage group A3 at the position of major QTL YL1 and ML1 and appeared orthologous to the t1 locus of the allotetraploids. Interestingly, a fiber mutation, sma-4(ha), observed in the same F(2) population cosegregated with the glabrous marker, which indicates either close linkage or common genetic control of lint fiber and leaf trichomes. Studies of A genome diploids may help to clarify the genetic control of trichomes and fiber in both diploid and tetraploid cottons.

Genome research promises to promote continued and enhanced plant genetic improvement. As a world's leading crop and a model system for studies of many biological processes, genomics research of cottons has advanced rapidly in the past few years. This article presents a comprehensive review on the recent advances of cotton genomics research. The reviewed areas include DNA markers, genetic maps, mapped genes and QTLs, ESTs, microarrays, gene expression profiling, BAC and BIBAC libraries, physical mapping, genome sequencing, and applications of genomic tools in cotton breeding. Analysis of the current status of each of the genome research areas suggests that the areas of physical mapping, QTL fine mapping, genome sequencing, nonfiber and nonovule EST development, gene expression profiling, and association studies between gene expression and fiber trait performance should be emphasized currently and in near future to accelerate utilization of the genomics research achievements for enhancing cotton genetic improvement.

Despite rapidly decreasing costs and innovative technologies, sequencing of angiosperm genomes is not yet undertaken lightly. Generating larger amounts of sequence data more quickly does not address the difficulties of sequencing and assembling complex genomes de novo. The cotton ( Gossypium spp.)

QTL mapping experiments yield heterogeneous results due to the use of different genotypes, environments, and sampling variation. Compilation of QTL mapping results yields a more complete picture of the genetic control of a trait and reveals patterns in organization of trait variation. A total of 432 QTL mapped in one diploid and 10 tetraploid interspecific cotton populations were aligned using a reference map and depicted in a CMap resource. Early demonstrations that genes from the non-fiber-producing diploid ancestor contribute to tetraploid lint fiber genetics gain further support from multiple populations and environments and advanced-generation studies detecting QTL of small phenotypic effect. Both tetraploid subgenomes contribute QTL at largely non-homeologous locations, suggesting divergent selection acting on many corresponding genes before and/or after polyploid formation. QTL correspondence across studies was only modest, suggesting that additional QTL for the target traits remain to be discovered. Crosses between closely-related genotypes differing by single-gene mutants yield profoundly different QTL landscapes, suggesting that fiber variation involves a complex network of interacting genes. Members of the lint fiber development network appear clustered, with cluster members showing heterogeneous phenotypic effects. Meta-analysis linked to synteny-based and expression-based information provides clues about specific genes and families involved in QTL networks.

Root-knot nematodes Meloidogyne incognita (Kofoid and White) can cause severe yield loss in cotton (Gossypium hirsutum L.). The objectives of this study were to determine the inheritance and genomic location of genes conferring root-knot nematode resistance in M-120 RNR, a highly resistant G. hirsutum line with the Auburn 623 RNR source of resistance. Utilizing two interspecific F(2) populations developed from the same M-120 RNR by Gossypium barbadense (cv. Pima S-6) cross, genome-wide scanning with RFLP markers revealed a marker on Chromosome 7 and two on Chromosome 11 showing significant association with the resistant phenotype. The association was confirmed using SSR markers with the detection of a minor and a major dominant QTL on Chromosome 7 and 11, respectively. Combined across the two populations, the major QTL on Chromosome 11 Mi-C11 had a LOD score of 19.21 (9.69 and 9.61 for Pop1 and Pop2, respectively) and accounted for 63.7% (52.6 and 65.56% for Pop1 and Pop2, respectively) of the total phenotypic variation. The minor QTL locus on Chromosome 7 Mi ( 1 ) -C07 had a LOD score of 3.48 and accounted for 7.7% of the total phenotypic variation in the combined dataset but was detected in only one population. The allele from the M-120 RNR parent contributed to increased resistance in the Mi-C11 locus, but surprisingly, the Pima S-6 allele contributed to increased resistance in the Mi-C07 locus. The M-120 RNR allele in the Mi-C11 locus, derived from the Auburn 623 RNR, is likely to have originated from the Clevewilt 6 cultivar. Results from this study indicated that the SSR marker CIR316 may replace the laborious greenhouse screening in breeding programs to identify genotypes resistant to M. incognita.

"The Cotton Diversity Database" (http://cotton.agtec.uga.edu) is a Web resource for cotton (Gossypium spp.) phenotypic and genomic data. A primary goal for this resource is to provide both a useful management tool for breeders and other applied scientists and a research tool for genetic and genomic scientists. The resource contains four interface suites that include displays for each of the available phenotypic or genomic data types. These display suites are accessible via the genotype portal, a search interface that allows users to begin with a cotton accession and obtain all available data. The phenotypic data displays include graphical views of overall cultivar performance with means and between group standard deviations indicated in an easy-to-interpret graphical manner for common trial measures such as lint yield, micronaire, etc. The genomic data displays include interactive graphical views of genetic map and diversity data types. Genetic map data is displayed in both traditional linear and two-dimensional comparative dot plot formats. Genetic diversity data is displayed in an interactive tree-based format showing degrees of similarity among genotypes. The data are stored in Oracle relational database (RDBMS) schemas containing tables and views for data storage, auto-calculated statistics and display parameters. The searchable RDBMS provides flexibility for a wide range of query and search options as well as integration paths amongst the various data types.

The genus Gossypium, which comprises a divergent group of diploid species and several recently formed allotetraploids, offers an excellent opportunity to study polyploid genome evolution. In this study, chromosome structural variation among the A, At, and D genomes of Gossypium was evaluated by comparative genetic linkage mapping. We constructed a fully resolved RFLP linkage map for the diploid A genome consisting of 275 loci using an F2interspecific Gossypium arboreum × Gossypium herbaceum family. The 13 chromosomes of the A genome are represented by 12 large linkage groups in our map, reflecting an expected interchromosomal translocation between G. arboreum and G. herbaceum. The A-genome chromosomes are largely collinear with the D genomes, save for a few small inversions. Although the 2 diploid mapping parents represent the closest living relatives of the allotetraploid At-genome progenitor, 2 translocations and 7 inversions were observed between the A and Atgenomes. The recombination rates are similar between the 2 diploid genomes; however, the Atgenome shows a 93% increase in recombination relative to its diploid progenitors. Elevated recombination in the Dtgenome was reported previously. These data on the Atgenome thus indicate that elevated recombination was a general property of allotetraploidy in cotton.Key words: comparative mapping, polyploidy, genome evolution, inversions, translocations, RFLP.

by different approaches, which include the use of pedigrees and DNA fingerprinting. The COP measures the Knowledge of genetic diversity and relationships among breeding degree of genetic relatedness among genotypes based materials is essential to the improvement of crop species. Genetic similarity estimates among cultivars are helpful to select parental on pedigree information by estimating the probability combinations for segregating populations so as to maintain genetic that a random allele from one genotype is identical by diversity in a breeding program. The objective of this study was to descent to a random allele of another genotype at the determine thecorrespondence between pedigree- andrestriction frag- same locus (Kempthorne, 1969). The accuracy of COP ment length polymorphism–based genetic similarity (RFLP-GS) esti- depends on the availability of reliable and detailed pedimatesforasetof36Uplandcotton(GossypiumhirsutumL.)cultivars. gree records; at times these records may be either unCoefficients of parentage (COPs) and genetic similarity estimates available or unreliable. The calculations also do not based on 261 codominant RFLP markers for all possible pairs of account for the effects of selection, mutation, and gecultivars were compared. A significant though moderate association netic drift and require several simplifying assumptions (r 0.41, P 0.001) was detected between the COP and RFLP-GS that are generally not met. Nevertheless, pedigree informatrices. Spearman’s rank correlationfor the142 pairsof related cultivars (COP 0.1) was somewhat higher (rS 0.53, P 0.001). There was mation offers plant breeders a simple and inexpensive a significant linear relationship between COP and RFLP-GS for the waytoestimategeneticrelatednessamongbreedingmapairs of related cultivars; however, the coefficient of determination terials. was low (R 2 0.25), indicating that the COP only explained a small DNA markers, such as RFLPs, amplified fragment portion of the variation observed for RFLP-GS. COP and RFLP-GS length polymorphisms (AFLPs), random amplified polyestimate different types of genetic resemblance; however, the moder- morphic DNAs (RAPDs), and simple sequence repeats ate association may have also resulted from violations to the assump- (SSRs), can directly assess DNA sequence variation. tions made when computing COP. RFLP-GS is a more accurate estimate DNA-based genetic similarity measures the degree of of true genetic resemblance among cotton cultivars. Nevertheless, the genetic relatedness among genotypes by estimating the pedigree- and RFLP-based dendrograms were somewhat similar, sugproportionof allelesthatare alikeinstate, thusdiffering gesting that pedigree information will continue to be useful to inexpensively identify diverse parents in a breeding program. from COP in the type of genetic resemblance estimated. As such, they provide a more precise estimate of genetic similarity among genotypes and do not require the assumptions inherent to pedigree analysis. All the DNA

A backcross-self population from a cross between Gossypium hirsutum and G. barbadense was used to dissect the molecular basis of genetic variation governing two parameters reflecting lint fiber fineness and to compare the precision of these two measurements. By applying a detailed restriction fragment length polymorphism (RFLP) map to 3,662 BC(3)F(2) plants from 24 independently derived BC(3) families, we were able to detect 32 and nine quantitative trait loci (QTLs) for fiber fineness and micronaire (MIC), respectively. The discovery of larger numbers of QTLs in this study than previously found in other studies based on F(2) populations grown in favorable environments reflects the ability of the backcross-self design to resolve smaller QTL effects. Although the two measurements differed dramatically in the number of QTLs detected, seven of the nine MIC QTLs were also associated with fiber fineness. This supports other data in suggesting that fiber fineness more accurately reflects the underlying physical properties of cotton fibers and, consequently, is a preferable trait for selection. "Negative transgression," with the majority of BC(3)F(2) families showing average phenotypes that were poorer than that of the inferior parent, suggests that many of the new gene combinations formed by interspecific hybridization are maladaptive and may contribute to the lack of progress in utilizing G. barbadense in conventional breeding programs to improve upland cotton.

The current study is the first installment of an effort to explore the secondary gene pool for the enhancement of Upland cotton (Gossypium hirsutum L.) germplasm. We developed advanced-generation backcross populations by first crossing G. hirsutum cv. Tamcot 2111 and G. barbadense cv. Pima S6, then independently backcrossing F(1) plants to the G. hirsutum parent for three cycles. Genome-wide mapping revealed introgressed alleles at an average of 7.3% of loci in each BC(3)F(1) plant, collectively representing G. barbadense introgression over about 70% of the genome. Twenty-four BC(3)F(1) plants were selfed to generate 24 BC(3)F(2) families of 22-172 plants per family (totaling 2,976 plants), which were field-tested for fiber elongation and genetically mapped. One-way analysis of variance detected 22 non-overlapping quantitative trail loci (QTLs) distributed over 15 different chromosomes. The percentage of variance explained by individual loci ranged from 8% to 28%. Although the G. barbadense parent has lower fiber elongation than the G. hirsutum parent, the G. barbadense allele contributed to increased fiber elongation at 64% of the QTLs. Two-way analysis of variance detected significant (P0.001) among-family genotype effects and genotypexfamily interactions in two and eight regions, respectively, suggesting that the phenotypic effects of some introgressed chromosomal segments are dependent upon the presence/absence of other chromosomal segments.

Improvement in somatic embryogenesis has been achieved in several cotton lines (Gossypium hirsutumL.) from the Georgia and Pee Dee germplasm with culture media containing various Putrescine concentrations. The best results were obtained with the α-naphthalene acetic acid (NAA)-based treatments, S15 g.05 NAA and EMMS2, as compared to the 2,4-dichlorophenoxyacetic acid (2,4-D)-based culture medium, EMMS4. Inclusion of 0.5 mg l−1 Putrescine improved somatic embryo (SE) induction for most treatments and lines tested. An 8-and 2-fold improvement was achieved in SE production on the EMMS2-0.5 Putrescine treatment as compared to EMMS2 alone for cotton lines PD 97019 and GA 98033, respectively. A significant increase in SE number (53-fold) was obtained with the addition of 0.5 mg l−1Putrescine to EMMS2 for PD 97021, which was essentially recalcitrant without Putrescine treatment. Conversion of SEs into plants was both genotype- and culture medium-dependent.

Summary The diploid cotton species can constitute a valuable gene pool for the more agronomically desirable cultivated tetraploid cultivars and offer better opportunities to study gene structure and function through gene knockouts. In order to exploit these advantages, a regeneration system is required to achieve these transformation-based goals. Carbohydrate source and concentration were evaluated to improve somatic embryo (SE) production and desiccation treatments to improve the conversion efficiency of SEs to plants in a diploid Gossypium arboreum accession, A2-9 (PI-529712). Improved SE numbers and their subsequent conversion into plantlets was achieved with a Murashige and Skoog (MS)/sucrose-based medium M2 [0.04 M sucrose, 0.3mM a-naphthaleneacetic acid (NAA)]. On this medium, 219 embryos per g initiated, and close to 11% of these embryos germinated into plantlets. Neither a 5-d desiccation treatment of embryogenic callus previously cultured in liquid medium nor filter paper insertion improved the numbers of SEs induced or their conversion to plantlets. A 3-d desiccation period resulted in improved plant regeneration. When immature G. arboreum SEs induced on M1 (0.2 M glucose, 2.6mM NAA, and 0.2mM kinetin) medium underwent a 3-d desiccation treatment, 49% of these immature SEs were converted to plantlets after a 4-wk period on M2 medium. These improved results will help to pave the way for future genetic transformation and associated gene structure and function studies utilizing G. arboreum. These results, in particular the 3-d desiccation treatment, can also be incorporated into regeneration protocols to improve the regeneration efficiency of other Gossypium species.

We report genetic maps for diploid (D) and tetraploid (AtDt) Gossypium genomes composed of sequence-tagged sites (STS) that foster structural, functional, and evolutionary genomic studies. The maps include, respectively, 2584 loci at 1.72-cM (∼600 kb) intervals based on 2007 probes (AtDt) and 763 loci at 1.96-cM (∼500 kb) intervals detected by 662 probes (D). Both diploid and tetraploid cottons exhibit negative crossover interference; i.e., double recombinants are unexpectedly abundant. We found no major structural changes between Dt and D chromosomes, but confirmed two reciprocal translocations between At chromosomes and several inversions. Concentrations of probes in corresponding regions of the various genomes may represent centromeres, while genome-specific concentrations may represent heterochromatin. Locus duplication patterns reveal all 13 expected homeologous chromosome sets and lend new support to the possibility that a more ancient polyploidization event may have predated the A-D divergence of 6–11 million years ago. Identification of SSRs within 312 RFLP sequences plus direct mapping of 124 SSRs and exploration for CAPS and SNPs illustrate the “portability” of these STS loci across populations and detection systems useful for marker-assisted improvement of the world's leading fiber crop. These data provide new insights into polyploid evolution and represent a foundation for assembly of a finished sequence of the cotton genome.

Grain protein concentration (GPC) is an important component of durum wheat (Triticum turgidum L. var. durum) quality. The 'Langdon'-Triticum turgidum L. var. dicoccoides chromosome 6B substitution line [LDN(DIC-6B)] contains the high GPC quantitative trait locus "QGpc.ndsu.6Bb." We evaluated the effect of this quantitative trait locus on GPC, grain yield, and other agronomic traits in an adapted durum wheat background, verified its location on chromosome 6B and determined its relationship to the GPC locus previously identified. A recombinant inbred population consisting of 110 lines segregating for high GPC was developed from the LDN(DIC-6B) with two doses of adapted germplasm. This population was evaluated in the field for GPC at two locations in 1995, and for GPC, grain yield, and other agronomic characteristics at three locations in 1996. Segregation analysis for GPC showed a bimodal distribution, indicating a single genetic factor or a tightly linked gene cluster controlling high GPC. This high GPC locus was insensitive to environmental conditions. Grain protein concentration was not correlated with plant height, but was loosely correlated with grain yield and heading date. Quantitative trait locus analysis using simple regression and interval mapping procedures identified a locus flanked by Xcdo365 and Xmwg79 on chromosome 6B as having a major effect on GPC. This high GPC locus, which explained up to 72% of the phenotypic variance, accounted for a 15 g kg-1 increase in average GPC. Selection for the two markers flanking the GPC QTL would be highly effective in introgressing this QTL into durum wheat breeding programs.

We report a second major QTL for root-knot nematode resistance in the highly resistant Upland cotton line M-120RNR and show epistasis between two resistant QTLs with different mechanisms conferring resistance. In an earlier study, we identified a major QTL on Chromosome 11 associated with resistance to root-knot nematode in the M-120 RNR Upland cotton line (Gossypium hirsutum L.) of the Auburn 623 RNR source. Herein, we re-evaluated the genetics of the resistance to root-knot nematode in the M-120 RNR × Pima S-6 population by linkage mapping using recently published SSR markers. The QTL analysis detected two regions significantly associated with the resistance phenotype. In addition to the QTL previously identified on Chromosome 11 (qMi-C11), a major QTL was identified on Chromosome 14 (qMi-C14). The resistance locus on qMi-C11 originated from the Clevewilt parent, while the qMi-C14 locus originated from the other resistant parent, Mexico Wild Jack Jones. The qMi-C14 locus had logarithms of odds score of 17 and accounted for 45 % of the total phenotype variation in egg production. It was also associated with galling index, but the percent variation explained was only 6 %, suggesting that the qMi-C11 locus had a much stronger effect on root gall suppression than egg production, while the qMi-C14 locus had a stronger effect on egg production than galling. The results also suggest that the transgressive segregation observed in the development of Auburn 623 RNR was due to the pyramiding of at least two main effect QTLs as well as an additive-by-additive epistatic effects between the two resistant loci. The SSRs markers tightly linked to the qMi-C11 and qMi-C14 loci will greatly facilitate the improvement of RKN resistance in cotton via marker-assisted breeding.

The theory of pivotal–differential evolution states that one genome of polyploid wheats remains stable (i.e., pivotal) during evolution, while the other genome or genomes may become modified (i.e., differential). A proposed mechanism for apparent modification of the differential genome is that different polyploid species with only one genome in common may exchange genetic material. In this study, we analyzed a set of sympatric and allopatric accessions of tetraploid wheats with the genomic constitutions UM and UC. The U genome of these species is from Triticum umbellulatum and is considered to be the pivotal genome. The M and C genomes, from T. comosum and T. dichasians, respectively, are considered to be the differential genomes. Low copy DNA was analyzed using "sequence tagged site" primer sets in the polymerase chain reaction, followed by digestion with restriction enzymes. Genetic similarity matrices based on shared restriction fragments showed that sympatric accessions of different U genome tetraploid species did not tend to share more restriction fragments than did allopatric accessions. Thus, no evidence for introgression was found. Analysis of the diploid progenitor species showed that the U genome was less variable than the M and C genomes. Additionally, comparison of diploid and polyploid species using genome-specific primer sets suggests a possible polyphyletic origin for T. triunciale and T. machrochaetum. Thus, our results suggest that the differential nature of the M and C genomes may be the result of variability introduced by the diploid progenitors and not the result of frequent introgression events after formation of the polyploid.Key words: wild wheat, evolution, introgression, PCR.

Polyploidy often confers emergent properties, such as the higher fibre productivity and quality of tetraploid cottons than diploid cottons bred for the same environments. Here we show that an abrupt five-to sixfold ploidy increase approximately 60million years (Myr) ago, and allopolyploidy reuniting divergent Gossypium genomes approximately 1-2 Myr ago, conferred about 30-36-fold duplication of ancestral angiosperm (flowering plant) genes in elite cottons (Gossypium hirsutum and Gossypium barbadense), genetic complexity equalled only by Brassica among sequenced angiosperms. Nascent fibre evolution, before allopolyploidy, is elucidated by comparison of spinnable-fibred Gossypium herbaceum A and non-spinnable Gossypium longicalyx F genomes to one another and the outgroup D genome of non-spinnable Gossypium raimondii. The sequence of a G. hirsutum A t D t (in which t' indicates tetraploid) cultivar reveals many non-reciprocal DNA exchanges between subgenomes that may have contributed to phenotypic innovation and/or other emergent properties such as ecological adaptation by polyploids. Most DNA-level novelty in G. hirsutum recombines alleles from the D-genome progenitor native to its New World habitat and the Old World A-genome progenitor in which spinnable fibre evolved. Coordinated expression changes in proximal groups of functionally distinct genes, including a nuclear mitochondrial DNA block, may account for clusters of cotton-fibre quantitative trait loci affecting diverse traits. Opportunities abound for dissecting emergent properties of other polyploids, particularly angiosperms, by comparison to diploid progenitors and outgroups. © 2012 Macmillan Publishers Limited. All rights reserved.

To explore types, levels and patterns of genetic divergence among diploid Gossypium (cotton) genomes, 780 cDNA, genomic DNA and simple sequence repeat (SSR) loci were re-sequenced in Gossypium herbaceum (A1 genome), G. arboreum (A2), G. raimondii (D5), G. trilobum (D8), G. sturtianum (C1) and an outgroup, Gossypioides kirkii. Divergence among these genomes ranged from 7.32 polymorphic base pairs per 100 between G. kirkii and G. herbaceum (A1) to only 1.44 between G. herbaceum (A1) and G. arboreum (A2). SSR loci are least conserved with 12.71 polymorphic base pairs and 3.77 polymorphic sites per 100 base pairs, whereas expressed sequence tags are most conserved with 3.96 polymorphic base pairs and 2.06 sites. SSR loci also exhibit the highest percentage of 'extended polymorphisms' (spanning multiple consecutive nucleotides). The A genome lineage was particularly rapidly evolving, with the D genome also showing accelerated evolution relative to the C genome. Unexpected asymmetry in mutation rates was found, with much more transition than transversion mutation in the D genome after its divergence from a common ancestor shared with the A genome. This large quantity of orthologous DNA sequence strongly supports a phylogeny in which A-C divergence is more recent than A-D divergence, a subject that is of much importance in view of A-D polyploid formation being key to the evolution of the most productive and finest-quality cottons. Loci that are monomorphic within A or D genome types, but polymorphic between genome types, may be of practical importance for identifying locus-specific DNA markers in tetraploid cottons including leading cultivars.

The polymerase chain reaction (PCR) is an attractive technique for many genome mapping and characterization projects. One PCR approach which has been evaluated involves the use of randomly amplified polymorphic DNA (RAPD). An alternative to RAPDs is the sequence-tagged-site (STS) approach, whereby PCR primers are designed from mapped low-copy-number sequences. In this study, we sequenced and designed primers from 22 wheat RFLP clones in addition to testing 15 primer sets that had been previously used to amplify DNA sequences in the barley genome. Our results indicated that most of the primers amplified sequences that mapped to the expected chromosomes in wheat. Additionally, 9 of 16 primer sets tested revealed polymorphisms among 20 hexaploid wheat genotypes when PCR products were digested with restriction enzymes. These results suggest that the STS-based PCR analysis will be useful for generation of informative molecular markers in hexaploid wheat.

The use of well-characterised, mapped DNA sequences was explored to prime polymerase chain reaction sequence amplification. Many of the markers that are been developed for use in genetic research are informative enough to be potentially useful in an industrial setting. Estimates of setup costs were also provided to utilise this technology and the throughput that could be expected of a laboratory facility managed by one worker

Field observations indicate that sulfonylurea- resistant kochia may germinate at lower soil temperatures and/or germinate more rapidly than susceptible kochia in the absence of herbicide. To investigate this possibility, seeds from three resistant and two susceptible kochia accessions were germinated at temperatures ranging from 4.6 to 13.2 C on thermal gradient plates. At 4.6 and 13.2 C, germination rates of all resistant accessions were higher than susceptible accessions, while germination rates of one resistant accession were higher than susceptible accessions at 7.2 and 10.5 C. Percent germina- tion of all resistant accessions was significantly higher than susceptible accessions after 48 h at 4.6 C. At higher temperatures, percent germination of some resistant accessions was higher after 12 or 24 h, but germination of all accessions was similar at later times. HPLC analysis revealed that seeds from resistant accessions contained about 2-fold higher free levels of branched chain amino acids than seeds from susceptible accessions. The results indicate that mutations conferring resistance to sul- fonylurea herbicides in these kochia accessions may concomitantly reduce or abolish acetolactate synthase sensitivity to normal feedback inhibition patterns, result- ing in elevated levels of branched chain amino acids available for cell division and growth during early germination. Nomenclature: Kochia, Kochia scoparia L. Schrad #3 KCHSC; chlorsulfuron, 2-chloro-N-(((4- methoxy-6-methyl-1,3,5-triazin-2-yl)amino)carbonyl)ben

Cotton is the single most important natural fiber in the world and represents a vital agricultural commodity in the global economy. Ninety percent of cotton’s value resides in the lint fiber. Cotton fiber quality, defined by the physical properties of the lint fibers, is an important part of the cotton manufacturing process from field harvest through ginning and textile manufacturing and is reflected in the end product. The primary fiber properties affecting textile manufacturing and end product quality include fiber length and uniformity, strength, elongation, fineness, and maturity. Numerous techniques and tools to measure these fiber properties have been developed during the last 100 years. Classical quantitative genetics research methods have determined the heritability, components of genetic variance, environmental interactions, and correlations of fiber properties among one another and with fiber yield. In response to the advances made in fiber processing and manufacturing over the course of the 20th and 21st centuries, classical plant breeding based on phenotypic selection has improved fiber quality while also increasing fiber yields. At the same time, intensive phenotypic selection programs have resulted in decreased levels of genetic diversity within the primary gene pool of Upland cotton. Classical plant breeding programs have faced challenges and difficulties transferring new, stably inherited allelic variation from inter-specific hybridization. However, the last 15 years have witnessed an explosion of efforts to utilize molecular biology tools to study the structure, function, and evolutionary relationships of the cotton genome. Much of the first 15 years of molecular genetic research into cotton fiber quality has been devoted to developing core infrastructure including polymorphic DNA markers, discrete genetic mapping populations, and extensive nuclear genetic linkage maps. This activity has provided insight into the location, effects, and complexity of the quantitative trait loci (QTL) associated with fiber properties. A fascinating story is being written from the advances being made by combining classical and molecular genetics to explore fiber quality. Although fiber properties are affected by a large number of small effect QTLs, molecular research has also demonstrated that a large percentage of the loci controlling fiber quality properties are present in “gene islands” that are non-randomly distributed across the A- and D-genomes. The next 15 years of molecular genetic research will undoubtedly provide a clearer picture of the genetic basis of cotton fiber quality and the functions of genes controlling various fiber properties. Future research efforts that combine the power of molecular genetics with the knowledge and experience accrued by classical plant breeding will provide portable and inexpensive DNA markers that can be used by plant breeders to select and develop the next generation of high fiber quality cotton cultivars.

The Gossypium genus has more than 50 species that are available to use as germplasm; 5 species, including G. hirsutum, are allotetraploids while the rest are diploid species. The 7 races of G. hirsutum are directly usable as a germplasm resource with photoperiodism as the main barrier. The sister tetraploids require further effort to be utilized as germplasm for G. hirsutum improvement due to segregational breakdown. Utilizing germplasm from the diploids generally requires more extreme methods such as chromosome doubling and the use of bridging species. The phenotypic consequences of the domestication of Upland cotton, G. hirsutum, are similar to the domestication syndrome that is generally common to many crop plants. The genetic consequences of domestication are reflected by the very low level of genetic diversity found in Upland cultivars. In continuing the domestication of Upland cotton, developmental breeding programs are quickly becoming absolutely imperative to provide the diversity that is needed to provide intrinsic genetic solutions to the needs of producers, processors, and consumers.

Fiber from cotton (Gossypium hirsutum and G. barbadense) is a major product in the world economy. It is a botanically unique plant as it is a perennial allotetraploid derived from diploid Gossypium species, one of which does not produce lint, which is grown as an annual row crop. Cotton is an especially appropriate system for research into the molecular basis of plant response to water deficit and salinity, as it originates from wild perennial plants adapted to semi-arid, sub-tropical environments which experienced periodic drought and temperature extremes that are associated with soils with high salt content. The current primary molecular breeding approaches include transgenic modification and quantitative trait mapping with marker-assisted selection. The preliminary work in QTL mapping for drought response and the relationships of the QTLs with the drought-associated measurements is developing a foundation for understanding and using the molecular basis of drought tolerance. QTL mapping for salt tolerance is not moving apace. Using and/or regulating transgene effects on the plant responses to drought and salinity has shown success and will continue to increase our understanding of the complexity of plant’s physiological pathways. Improvements in all areas of molecular breeding are almost certain, but the most effective improvements will come from exploiting our improved understanding of the genetic architecture

Mapping of genes that play major roles in cotton fiber development is an important step toward their cloning and manipulation, and provides a test of their relationships (if any) to agriculturally-important QTLs. Seven previously identified fiber mutants, four dominant (Li 1, Li 2, N 1 and Fbl) and three recessive (n 2, sma-4(h a), and sma-4(fz)), were genetically mapped in six F2 populations comprising 124 or more plants each. For those mutants previously assigned to chromosomes by using aneuploids or by linkage to other morphological markers, all map locations were concordant except n 2, which mapped to the homoeolog of the chromosome previously reported. Three mutations with primary effects on fuzz fibers (N 1, Fbl, n 2) mapped near the likelihood peaks for QTLs that affected lint fiber productivity in the same populations, perhaps suggesting pleiotropic effects on both fiber types. However, only Li 1 mapped within the likelihood interval for 191 previously detected lint fiber QTLs discovered in non-mutant crosses, suggesting that these mutations may occur in genes that played early roles in cotton fiber evolution, and for which new allelic variants are quickly eliminated from improved germplasm. A close positional association between sma-4(h a ), two leaf and stem-borne trichome mutants (t 1 , t 2), and a gene previously implicated in fiber development, sucrose synthase, raises questions about the possibility that these genes may be functionally related. Increasing knowledge of the correspondence of the cotton and Arabidopsis genomes provides several avenues by which genetic dissection of cotton fiber development may be accelerated.

A backcross-self population from a cross between Gossypium hirsutum and G. barbadense was used to dissect the molecular basis of genetic variation governing 15 parameters that reflect fiber length. Applying a detailed restriction fragment length polymorphism (RFLP) map to 3,662 BC(3)F(2) plants from 24 independently derived BC(3) families, we detected 28, nine, and eight quantitative trait loci (QTLs) for fiber length, length uniformity, and short fiber content, respectively. For eight, six, and two chromosomal regions containing quantitative trait loci (QTLs) for fiber length, length uniformity, and short fiber content (respectively), two-way analysis of variance showed a significant (P0.001) among-family genotypic effect. A total of 13, two, and four loci showed genotype x family interaction, illustrating some of the complexities that are likely to be faced in introgression of exotic germplasm into the gene pool of cultivated cotton. Co-location of many QTLs for fiber length, length uniformity, and short fiber content accounted for correlations among these traits, while the discovery of many QTLs unique to each trait suggests that maximum genetic gain will require breeding efforts that target each trait (or an index including all three). The availability of DNA markers linked to G. barbadense QTLs identified in this and other studies promise to assist breeders in transferring and maintaining valuable traits from exotic sources during cultivar development.

We investigated the utility of the Gossypium arboreum EST sequences in the GenBank database for develop- ing PCR-based markers targeting known-function genes in cultivated tetraploid cottons, G. hirsutum and G. barbadense. Four hundred sixty-five randomly selected ESTs from this library were subjected to BLASTn search against all GenBank databases, of which putative function was assigned to 93 ESTs based on high nucleotide homology to previ- ously studied genes. PCR primers were synthesized for 89 of the known-function ESTs. A total of 57 primer pairs am- plified G. arboreum genomic DNA, but only 39 amplified in G. hirsutum and G. barbadense, suggesting that sequence divergence may be a factor causing non-amplification for some sites. DNA sequence analysis showed that most primer pairs were targeting the expected homologous loci. While the amplified products that were of larger size than the cor- responding EST sequences contain introns, the primer pairs with a smaller amplicon than predicted from the flanking EST sequences did not amplify the expected orthologous gene sequences. Among the 39 primer pairs that amplified tetraploid cotton DNA, 3 detected amplicon size polymorphisms and 10 detected polymorphisms after digestion with one of six restriction enzymes. Ten of the polymorphic loci were subsequently mapped to an anchor RFLP map. Diges- tion of PCR-amplified sequences offers one means by which cotton genes can be mapped to their chromosomal loca- tions more quickly and economically than by RFLP analysis. Resume : Les auteurs ont explore la possibilite d'exploiter les sequences EST provenant du Gossypium arboreum dis- ponibles dans GenBank pour developper des marqueurs PCR correspondant a des genes de fonction connue chez les cotonniers tetraploides G. hirsutum et G. barbadense. Quatre-cent-soixante-cinq EST choisis au hasard ont fait l'objet d'une analyse BLASTN contre toutes les banques de donnees de GenBank. Une fonction putative a ete assignee a 93 EST sur la base d'une tres forte homologie a des genes etudies auparavant. Des amorces PCR ont ete synthetisees pour 89 de ces sequences de fonction connue. De celles-ci, 57 paires d'amorces ont produit un amplicon avec l'ADN geno- mique du G. arboreum alors que seulement 39 ont produit des amplicons avec l'ADN genomique du G. hirsutum ou du G. barbadense. Ces observations suggerent que de la divergence nucleotidique a rendu impossible l'amplification de certains locus. Une analyse des sequences d'ADN a montre que la plupart des amplicons correspondaient aux homolo- gues attendus. Les amplicons de taille superieure a l'attente contenaient des introns alors que les amplicons de taille in- ferieure ne correspondaient pas aux sequences orthologues attendues. Des 39 paires qui ont produit des amplicons chez le cotonnier tetraploide, trois ont produit du polymorphisme de taille et 10 autres montraient un polymorphisme suite a la digestion avec l'une des six enzymes employees. Dix des locus polymorphes ont ete ensuite situes sur une carte ge- netique a base de marqueurs RFLP. La digestion d'amplicons constitue une approche par laquelle des genes peuvent se voir assigner une position chromosomique plus rapidement et economiquement que par analyse RFLP.

The US cotton production system exemplifiesthe complex challenges that must be met in orderto reduce the genetic vulnerability of a majorcrop.Genetic vulnerability results from acombination of a crop’s evolutionary history,trends in breeding and biotechnology practices,and grower Decisions based on inadequateinformation being available,all in response tothe inevitable pressures imposed by processor

Molecular markers such as simple sequence repeats (SSR) are a useful tool for characterizing genetic diversity of Gossypium germplasm. Genetic profiles by DNA fingerprinting of cotton accessions can only be compared among different collections if a common set of molecular markers are used by different laboratories and/or research projects. Herein, we propose and report a core set of 105 SSR markers with wide genome coverage of at least four evenly distributed markers per chromosome for the 26 tetraploid cotton chromosomes. The core marker set represents the efforts of ten research groups involved in marker development, and have been systematically evaluated for DNA polymorphism on the 12 genotypes belonging to six Gossypium species [known collectively as the cotton marker database (CMD) panel]. A total of 35 marker bins in triplex sets were arranged from the 105 markers that were each labeled with one of the three fluorescent dyes (FAM, HEX, and NED). Results from this study indicated that the core marker set was robust in revealing DNA polymorphism either between and within species. Average value of polymorphism information content (PIC) among the CMD panel was 0.65, and that within the cultivated cotton species Gossypium hirsutum was 0.29. Based on the similarity matrix and phylogenetic analysis of the CMD panel, the core marker set appeared to be sufficient in characterizing the diversity within G. hirsutum and other Gossypium species. The portability of this core marker set would facilitate the systematic characterization and the simultaneous comparison among various research efforts involved in genetic diversity analysis and germplasm resource preservation.

Pathogens are imminent threats to crop production. Among the management tools available to protect crops from diseases, the use of host-plant resistance had been hindered by a lack of tools and resources to identify resistance genes (R-genes). Genomic technologies have empowered acquisition of a new level and quality of information on plant-pathogen interactions. Next generation sequencing, differential transcriptome analysis, gene editing, and use of bioinformatics have greatly expanded the numbers of R-genes identified, enriched understanding of R-avirulence gene interactions, and disease diagnosis. In this review, we highlight the application of genomic technologies to identification of pathogen machinery for future improvement of host plant resistance. Made available in DSpace on 2020-01-14T18:12:58Z (GMT). No. of bitstreams: 1 Hostpathogenwars.pdf: 352779 bytes, checksum: 5ee70c598b4652f917fe3f8e5f2abaca (MD5) Previous issue date: 2019