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Cotton (Gossypium L.) is the most important fiber crop worldwide. Here, transcriptome analysis was conducted on developing fibers of a G. mustelinum introgression line, IL9, and its recurrent parent, PD94042, at 17 and 21 days post-anthesis (dpa). Differentially expressed genes (DEGs) of PD94042 and IL9 were identified. Gene Ontology (GO) enrichment analysis showed that the annotated DEGs were rich in two main biological processes and two main molecular functions. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis likewise showed that the annotated DEGs were mainly enriched in metabolic pathways and biosynthesis of secondary metabolites. In total, 52 DEGs were selected as candidate genes based on comparison of the DEGs and GO function annotation information. Quantitative real-time PCR (RT-qPCR) analysis results for 12 randomly selected DEGs were consistent with transcriptome analysis. SNP identification based on G. mustelinum chromatin segment introgression showed that 394 SNPs were identified in 268 DEGs, and two genes with known functions were identified within fiber strength quantitative trait loci (QTL) regions or near the confidence intervals. We identified 52 key genes potentially related to high fiber strength in a G. mustelinum introgression line and provided significant insights into the study of cotton fiber quality improvement.

Gene introgression from wild species has been shown to be a feasible approach for fiber quality improvement in Upland cotton. Previously, we developed an interspecific G. mustelinum × G. hirsutum advanced-backcross population and mapped over one hundred QTL for fiber quality traits. In the current study, a trait-based selective genotyping approach was utilized to prioritize a small subset of introgression lines with high phenotypic values for different fiber quality traits, to simultaneously validate multiple fiber quality QTL in a single experiment. A total of 75 QTL were detected by CIM and/or single-marker analysis, including 11 significant marker-trait associations (P < 0.001) and three putative associations (P < 0.005) also reported in earlier studies. The QTL that have been validated include three each for fiber length, micronaire, and elongation, and one each for fiber strength and uniformity. Collectively, about 10% of the QTL previously reported have been validated here, indicating that selective genotyping has the potential to validate multiple marker-trait associations for different traits, especially those with a moderate to large-effect detected simultaneously in one experimental population. The G. mustelinum alleles contributed to improved fiber quality for all validated loci. The results from this study will lay the foundation for further fine mapping, marker-assisted selection and map-based gene cloning.

Eight upland cotton (Gossypium hirsutum L.) germplasm lines, GA qFL25-A1 (Reg.no. GP-1063, PI 690458), GA qFL25-A2 (Reg. no. GP-1064, PI 690459), GA qFL25-P1 (Reg. no. GP-1066, PI 690461), GA qFL25-P2 (Reg. no. GP-1065, PI 690460), GA qFL25-D1 (Reg. no. GP-1070, PI 690465), GA qFL25-D2 (Reg. no. GP-1069, PI 690464), GA qFL25-G1 (Reg. no. GP-1068, PI 690463), and GA qFL25-G2 (Reg. no. GP-1067, PI 690462), were developed by the Molecular Cotton Breeding Laboratory, Department of Crop and Soil Sciences, at the University of Georgia in Tifton, GA. These eight germplasm lines resulted from crossing 'Sealand 883' (SL883), a G. hirsutum line with significant introgression from G. barbadense L., with four diverse G. hirsutum parents, 'Acala SJ-4', 'Paymaster HS 26', 'Deltapine 50', andGA 2004089, an unreleased breeding line. Previous work identified qFL-Chr.25, a quantitative trait locus (QTL) inherited from G. barbadense with significant effect on fiber upper-half mean length (FL) carried by SL883. Bulked sister lines were selected with the aid of marker-assisted selection from several F3:5 segregating families from each of these four cross combinations to quantify the effect of the allele in sister lines with and without the QTL. The presence of the SL883 allele for qFL-Chr.25 resulted in FL increases of 0.6 mm (1.9%) to 3.5 mm (11.7%) compared with the corresponding sister lines without the QTL. These eight lines should be useful for marker-assisted improvement of fiber length Made available in DSpace on 2022-02-11T02:02:35Z (GMT). No. of bitstreams: 1 RESGISTRATION-OF-EIGTH-UPLANT-COTTON.pdf: 204323 bytes, checksum: 08da3d8da8da5c54f40d8e37ffc3a2ff (MD5) Previous issue date: 2020

Quantitative trait loci (QTLs) qMi-C11 and qMi-C14 impart a high level of resistance to Meloidogyne incognita in cotton. Breeders had previously backcrossed both QTLs into the susceptible Coker 201 to create the highly resistant M-120 RNR, and we crossed Coker 201 and M-120 RNR to create near-isogenic lines with either qMi-C11 or qMi-C14. Previous work suggests different modes of action for qMi-C11 and qMi-C14. To document individual and combined effects of the QTLs on nematode development and reproduction, Coker 201 (neither QTL), M-120 RNR (both QTLs), CH11 near isoline (qMi-C11), and CH14 near isoline (qMi-C14) were inoculated with M. incognita. At 4, 8, 12, 16, 20, 25, and 30 days after inoculation (DAI), roots were stained to observe nematode developmental stages (second-stage juvenile [J2], swollen second-stage juvenile [SJ2], third-stage juvenile [J3], fourth-stage juvenile [J4], and female), and the number of galls was counted. At 20, 25, 30, and 40 DAI, M. incognita eggs were harvested and counted. At 30 DAI, 80% of the nematodes on Coker 201 were female compared with 50, 40, and 33% females on CH14, CH11, and M-120 RNR, respectively, and greater proportions of nematodes remained in J2 in M-120 RNR (41%), CH11 (58%), and CH14 (27%) than in Coker 201 (9%). More nematodes progressed to J3 or J4 on Coker 201 and CH14 than on CH11 or M-120 RNR. Coker 201 and CH14 had more galls than M-120 RNR. Coker 201 had more eggs than the other genotypes at 30 DAI. Nematode development beyond J2 or SJ2 was significantly reduced by qMi-C11, and development beyond J3 or J4 was significantly reduced by qMi-C14. This study confirms that qMi-C11 and qMi-C14 act at different times and have different effects on the development of M. incognita, and therefore, they have different modes of action.

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.

Cotton is widely grown in the southern US and Meloidogyne incognita is its most significant pathogen. The germplasm line M-120 RNR is highly resistant to M. incognita due to two resistance QTLs (quantitative trait loci), qMi-C11 and qMi-C14. Both QTLs reduce total egg production, but the QTLs affect M. incognita development at different life stages. The QTLs do not appear to affect initial penetration of M. incognita but genotypes containing qMi-C11 had fewer nematodes in the roots 8 days after inoculation than near isolines without qMi-C11, which may indicate M. incognita egression from roots. Three greenhouse trials were conducted using cotton isolines to determine whether qMi-C11 and qMi-C14 affect egression of M. incognita juveniles from roots. On each of the five sampling dates (4, 6, 8, 10, and 12 DAI), nematodes that egressed from roots were counted and roots were stained to count nematodes that remained in the roots. The effect of resistance QTLs on M. incognita egression from the roots differed among the trials. Nematode egression was consistently numerically greater, but inconsistently statistically different, from plants with both QTLs than from plants with neither QTL. Plants with only one QTL generally did not differ from plants with both QTLs, and the effects of qMi-C11 and qMi-C14 did not differ in any consistent way. In a separate experiment, plants with neither QTL had more eggs per egg mass than did plants with both QTLs, whereas plants with only one QTL had an intermediate number. Root gall size was measured in two trials and no consistent differences in gall size were observed. We conclude that (1) qMi-C11 and qMi-C14 do not stimulate nematode egression from cotton roots, (2) both qMi-C11 and qMi-C14 reduce M. incognita eggs/egg mass, and (3) neither qMi-C11 nor qMi-C14 affect gall size.

The Gossypium genus consists of about 50 diploid species distributed in 8 genome groups (A–G and K) and 7 known tetraploid species derived from the fusion of the A and D genomes. Recently, the genomes of allotetraploid cotton and its progenitors have been sequenced. Cotton (Gossypium sp.) is grown primarily for fiber and to a lesser extent its oilseed. The phenolic compound, gossypol, needs to be removed to make cottonseed oil edible. The oil composition is approximately two-thirds unsaturated to one-third saturated fatty acids. Understanding the genetic network of oil production and genes related to oil traits is important to develop a healthy edible product to fight global food scarcity. Studies pertaining to structural variation in genome and positional cloning have increased with the availability of genome sequence, enormous -omics data, and current low-cost next-generation sequencing techniques. Further, with the availability of functional verification tools like RNA-Seq and gene editing via RNAi or CRISPR/CAS9, one can effectively decipher the function of gene/s and their role in complex biosynthesis process of oil production. Whole-genome sequencing will serve as a foundation in developing cotton germplasm that can improve cottonseed oil without disturbing lint yield components.

Cotton leafroll dwarf virus (CLRDV) is an emerging virus in cotton production in Georgia and several other Southeastern states in the USA. To better understand the genetic diversity of the virus population, the near complete genome sequences of six isolates from Georgia and one from Alabama were determined. The isolates sequenced were 5,866 nucleotides with seven open reading frames (ORFs). The isolates from Georgia were >94% identical with other isolates from the USA and South America. In the silencing suppressor protein (P0), at amino acid position 72, the isolates from Georgia and Alabama had a valine (V), similar to resistant-breaking ‘atypical’ genotypes in South America, while the Texas isolate had isoleucine (I), similar to the more aggressive ‘typical’ genotypes of CLRDV. At position 120, arginine (R) is unique to Georgia and China isolates, but absent in Alabama, Texas and South American isolates. Ten potential recombinant events were detected in the isolates sequenced. An increased understanding of CLRDV population structure and genetic diversity will help develop management strategies for CLRDV in the USA cotton belt.

Three-dimensional (3D) point cloud based plant phenotyping facilitates the extraction of the structural information of phenotypic traits and reduces the effects of occlusion. In this study, we describe a cotton plant architectural component segmentation and phenotypic trait extraction method. Point cloud data of cotton plants were collected using a terrestrial LiDAR. Individual branches were segmented using a cylinder-fitting method. Next, plant architectural phenotypic traits were extracted at both plant and branch levels, including plant volume, branch length, diameter, volume, and branch angle. Two cotton plants with different shapes were used to demonstrate the performance of the proposed method. Results demonstrated that the method could process plants with not only an upright main stem but also a lodged main stem and the extracted phenotypic traits were reasonable. The proposed method could provide useful information and improve efficiency for plant breeding studies.

QTLs for fiber length mapped in three generations of advanced backcross populations derived from crossing Gossypium hirsutum and Gossypium mustelinum showed opportunities to improve elite cottons by introgression from wild relatives. The molecular basis of cotton fiber length in crosses between Gossypium hirsutum and Gossypium mustelinum was dissected using 21 BC3F2 and 12 corresponding BC3F2:3 and BC3F2:4 families. Sixty-five quantitative trait loci (QTLs) were detected by one-way analysis of variance. The QTL numbers detected for upper-half mean length (UHM), fiber uniformity index (UI), and short fiber content (SFC) were 19, 20, and 26 respectively. Twenty-three of the 65 QTLs could be detected at least twice near adjacent markers in the same family or near the same markers across different families/generations, and 32 QTLs were detected in both one-way variance analyses and mixed model-based composite interval mapping. G. mustelinum alleles increased UHM and UI and decreased SFC for five, one, and one QTLs, respectively. In addition to the main-effect QTLs, 17 epistatic QTLs were detected which helped to elucidate the genetic basis of cotton fiber length. Significant among-family genotypic effects were detected at 18, 16, and 16 loci for UHM, UI, and SFC, respectively. Six, two, and two loci showed genotype × family interaction for UHM, UI and SFC, respectively, illustrating complexities that might be faced in introgression of exotic germplasm into cultivated cotton. Co-location of many QTLs for UHM, UI, and SFC accounted for correlations among these traits, and selection of these QTLs may improve the three traits simultaneously. The simple sequence repeat (SSR) markers associated with G. mustelinum QTLs will assist breeders in transferring and maintaining valuable traits from this exotic source during cultivar development.

Pod and seed size are important characteristics for the peanut industry and have been under strong selection pressure since peanut domestication. In order to dissect the genetic control of peanut pod and seed size, a recombinant inbred mapping population from a cross of Florida-07 by GP-NC WS 16 was used to determine the genomic regions associated with traits including 100 pod weight, 100 seed weight, pod weight of double-seeded pods, seed weight of double-seeded pods, and area of double-seeded pods. Nine QTL on linkage groups (LGs) A05, A06, A09, B10, B04, A03, B05, and B08 were associated with pod and seed size. A majority of the QTL have small effects except the locus on LG A05 (93 to 102 Mbp) which explained up to 66% phenotypic variation for all measured pod and seed traits. A comparison of QTL previously reported for yield component traits showed a common QTL on LG A05 was detected in two genetic populations whose parentage is distinct from those used in this study. The markers tightly linked to this major QTL were informative in distinguishing large versus small-seeded germplasm lines in the mini core collection originating from thirty-one countries, suggesting selection for this seed size QTL in large-seeded ecotypes. However, the large seed size allele appeared to co-segregate with a late leaf spot disease susceptibility allele inherited from the Florida-07 parent. Therefore, peanut breeders need to weigh the pros and cons before integrating the large seed size QTL from Florida-07 in their breeding program.

Early and late leaf spots are the major foliar diseases of peanut responsible for severely decreased yield in the absence of intensive fungicide spray programs. Pyramiding host resistance to leaf spots in elite cultivars is a sustainable solution to mitigate the diseases. In order to determine the genetic control of leaf spot disease resistance in peanut, a recombinant inbred line population (Florida-07 x GP-NC WS16) segregating for resistance to both diseases was used to construct a SNP-based linkage map consisting of 855 loci. QTL mapping revealed three resistance QTLs for late leaf spot qLLSA05 (phenotypic variation explained, PVE=7-10%), qLLSB03 (PVE=5-7%), and qLLSB05 (PVE=15-41%) that were consistently expressed over multi-year analysis. Two QTL, qLLSA05 and qLLSB05, confirmed our previously published QTL-seq results. For early leaf spot, three resistance QTLs were identified in multiple years, two on chromosome A03 (PVE=8-12%) and one on chromosome B03 (PVE=13-20%), with the locus qELSA03_1.1 coinciding with the previously published genomic region for LLS resistance in GPBD4. Comparative analysis of the genomic regions spanning the QTLs suggests that resistance to early and late leaf spots are largely genetically independent. In addition, QTL analysis on yield showed that the presence of resistance allele in qLLSB03 and qLLSB05 loci might result in protection from yield loss caused by LLS disease damage. Finally, post hoc analysis of the RIL subpopulation that was not utilized in the QTL mapping revealed that the flanking markers for these QTLs can successfully select for resistant and susceptible lines, confirming the effectiveness of pyramiding these resistance loci to improve host-plant resistance in peanut breeding programs using marker-assisted selection.

Host plant resistance is the most practical approach to control the Southern root-knot nematode (Meloidogyne incognita; RKN), which has emerged as one of the most serious economic pests of Upland cotton (Gossypium hirsutum L.). Previous QTL analyses have identified a resistance locus on chromosome 11 (qMi-C11) affecting galling and another locus on chromosome-14 (qMi-C14) affecting egg production. Although these two QTL regions were fine mapped and candidate genes identified, expression profiling of genes would assist in further narrowing the list of candidate genes in the QTL regions. We applied the comparative transcriptomic approach to compare expression profiles of genes between RKN susceptible and resistance genotypes at an early stage of RKN development that coincides with the establishment of a feeding site and at the late stage of RKN development that coincides with RKN egg production. Sequencing of cDNA libraries produced over 315 million reads of which 240 million reads (76%) were mapped on to the Gossypium hirsutum genome. A total of 3,789 differentially expressed genes (DEGs) were identified which were further grouped into four clusters based on their expression profiles. A large number of DEGs were found to be down regulated in the susceptible genotype at the late stage of RKN development whereas several genes were up regulated in the resistant genotype. Key enriched categories included transcription factor activity, defense response, response to phyto-hormones, cell wall organization, and protein serine/threonine kinase activity. Our results also show that the DEGs in the resistant genotype at qMi-C11 and qMi-C14 loci displayed higher expression of defense response, detoxification and callose deposition genes, than the DEGs in the susceptible genotype.

Among the seven tetraploid cotton species, little is known about transmission genetics and genome organization in Gossypium mustelinum, the species most distant from the source of most cultivated cotton, G. hirsutum. In this research, an F2 population was developed from an interspecific cross between G. hirsutum and G. mustelinum (HM). A genetic linkage map was constructed mainly using simple sequence repeat (SSRs) and restriction fragment length polymorphism (RFLP) DNA markers. The arrangements of most genetic loci along the HM chromosomes were identical to those of other tetraploid cotton species. However, both major and minor structural rearrangements were also observed, for which we propose a parsimony-based model for structural divergence of tetraploid cottons from common ancestors. Sequences of mapped markers were used for alignment with the 26 scaffolds of the G. hirsutum draft genome, and showed high consistency. Quantitative trait locus (QTL) mapping of fiber elongation in advanced backcross populations derived from the same parents demonstrated the value of the HM map. The HM map will serve as a valuable resource for QTL mapping and introgression of G. mustelinum alleles into G. hirsutum, and help clarify evolutionary relationships between the tetraploid cotton genomes.

Premise of the study Introgression is widely acknowledged as a potential source of valuable genetic variation, and growing effort is being invested in analysis of interspecific crosses conferring transgressive variation. Experimental backcross populations provide an opportunity to study transmission genetics following interspecific hybridization, identifying opportunities and constraints to introgressive crop improvement. The evolutionary consequences of introgression have been addressed at the theoretical level, however, issues related to levels and patterns of introgression among (plant) species remain inadequately explored, including such factors as polyploidization, subgenome interaction inhabiting a common nucleus, and the genomic distribution and linkage relationships of introgressant alleles. Methods We analyze introgression into the polyploid Gossypium hirsutum (upland cotton) from its sister G. tomentosum and compare the level and pattern with that of G. barbadense representing a different clade tracing to the same polyploidization. Key results Across the genome, recurrent backcrossing to Gossypium hirsutum yielded only one-third of the expected average frequency of the G. tomentosum allele, although one unusual region showed preferential introgression. Although a similar rate of introgression is found in the two subgenomes of polyploid (AtDt) G. hirsutum, a preponderance of multilocus interactions were largely within the Dt subgenome. Conclusions Skewed G. tomentosum chromatin transmission is polymorphic among two elite G. hirsutum genotypes, which suggests that genetic background may profoundly affect introgression of particular chromosomal regions. Only limited correspondence is found between G. hirsutum chromosomal regions that are intolerant to introgression from the two species, G. barbadense and G. tomentosum, concentrated near possible inversion polymorphisms. Complex transmission of introgressed chromatin highlights the challenges to utilization of exotic germplasm in crop improvement.

The molecular genetic basis of cotton fiber strength and fineness in crosses between Gossypium mustelinum and Gossypium hirsutum (Upland cotton) was dissected using 21 BC3F2 and 12 corresponding BC3F2:3 and BC3F2:4 families. The BC3F2 families were genotyped with simple sequence repeat markers from a G. hirsutum by G. mustelinum linkage map, and the three generations of BC3-derived families were phenotyped for fiber strength (STR) and fineness (Micronaire, MIC). A total of 42 quantitative trait loci (QTLs) were identified through one-way analysis of variance, including 15 QTLs for STR and 27 for MIC, with the percentage of variance explained by individual loci averaging 13.86 and 14.06%, respectively. Eighteen of the 42 QTLs were detected at least twice near the same markers in different generations/families or near linked markers in the same family, and 28 of the 42 QTLs were identified in both mixed model-based composite interval mapping and one-way variance analyses. Alleles from G. mustelinum increased STR for eight of 15 and reduced MIC for 15 of 27 QTLs. Significant among-family genotypic effects (P < 0.001) were detected in 13 and 10 loci for STR and MIC respectively, and five loci showed significant (P < 0.001) genotype × family interaction for MIC. These results support the hypothesis that fiber quality improvement for Upland cotton could be realized by introgressing G. mustelinum alleles although complexities due to the different effects of genetic background on introgressed chromatin might be faced. Building on prior work with G. barbadense, G. tomentosum, and G. darwinii, QTL mapping involving introgression of G. mustelinum alleles offers new allelic variation to Upland cotton germplasm.

Introgressive breeding to introduce both obvious variation into a gene pool, and to unmask cryptic variation masked by close linkage or epistatic interactions, has repeatedly been attempted to improve fiber traits in Gossypium hirsutum by employing Gossypium barbadense as a donor parent. This study reports genetic variation for fiber quality traits in reciprocal advanced backcross populations between G. hirsutum cultivar Acala Maxxa and G. barbadense cultivar Pima S6. Micronaire (MIC), elongation (ELO), strength (STR), upper half mean length (UHM), and uniformity index (UI) showed significant genotypic variance, albeit different in the respective backgrounds for all traits except UI. Different levels of variation among genotypes for the same traits in reciprocal backgrounds suggest different levels of epistatic interactions, a hypothesis supported by a significant difference in transgressive segregants in Acala Maxxa and Pima S6 backgrounds. In Acala Maxxa background, 18, 18, 7, and 3 genotypes had significantly better MIC, ELO, STR and UHM, respectively, than Acala Maxxa. In Pima S6 background 10, 5, 8, and 11 genotypes had significantly better MIC, ELO, STR, and UHM, respectively, than Pima S6. Increased genetic variation and improved fiber quality in both backgrounds appears attainable using reciprocal introgression; however, the number of genotypes with simultaneous improvement for multiple fiber quality traits was higher in Acala Maxxa than Pima S6 background. Reciprocal populations provide a platform to study cytoplasmic effects on genetic variation and heritability of fiber quality traits, and estimate the size of base populations required to obtain genotypes with genetic gain by backcross breeding.

MicroRNAs (miRNAs) are small 20-24nt molecules that have been well studied over the past decade due to their important regulatory roles in different cellular processes. The mature sequences are more conserved across vast phylogenetic scales than their precursors and some are conserved within entire kingdoms, hence, their loci and function can be predicted by homology searches. Different studies have been performed to elucidate miRNAs using de novo prediction methods but due to complex regulatory mechanisms or false positive in silico predictions, not all of them express in reality and sometimes computationally predicted mature transcripts differ from the actual expressed ones. With the availability of a complete genome sequence of Gossypium arboreum, it is important to annotate the genome for both coding and noncoding regions using high confidence transcript evidence, for this cotton species that is highly resistant to various biotic and abiotic stresses. Here we have analyzed the small RNA transcriptome of G. arboreum leaves and provided genome annotation of miRNAs with evidence from miRNA/miRNA* transcripts. A total of 446 miRNAs clustered into 224 miRNA families were found, among which 48 families are conserved in other plants and 176 are novel. Four short RNA libraries were used to shortlist best predictions based on high reads per million (RPM). The size, origin, copy numbers and transcript depth of all miRNAs along with their isoforms and targets has been reported. The highest gene copy number was observed for gar-miR7504 followed by gar-miR166, gar-miR8771, gar-miR156 and gar-miR7484. Altogether, 1274 target genes were found in G. arboreum that are enriched for 216 KEGG pathways. The resultant genomic annotations are provided in UCSC, BED format.

This study reports transmission genetics of chromosomal segments into Gossypium hirsutum from its most distant euploid relative, Gossypium mustelinum . Mutilocus interactions and structural rearrangements affect introgression and segregation of donor chromatin. Wild allotetraploid relatives of cotton are a rich source of genetic diversity that can be used in genetic improvement, but linkage drag and non-Mendelian transmission genetics are prevalent in interspecific crosses. These problems necessitate knowledge of transmission patterns of chromatin from wild donor species in cultivated recipient species. From an interspecific cross, Gossypium hirsutum × Gossypium mustelinum, we studied G. mustelinum (the most distant tetraploid relative of Upland cotton) allele retention in 35 BC3F1 plants and segregation patterns in BC3F2 populations totaling 3202 individuals, using 216 DNA marker loci. The average retention of donor alleles across BC3F1 plants was higher than expected and the average frequency of G. mustelinum alleles in BC3F2 segregating families was less than expected. Despite surprisingly high retention of G. mustelinum alleles in BC3F1, 46 genomic regions showed no introgression. Regions on chromosomes 3 and 15 lacking introgression were closely associated with possible small inversions previously reported. Nonlinear two-locus interactions are abundant among loci with single-locus segregation distortion, and among loci originating from one of the two subgenomes. Comparison of the present results with those of prior studies indicates different permeability of Upland cotton for donor chromatin from different allotetraploid relatives. Different contributions of subgenomes to two-locus interactions suggest different fates of subgenomes in the evolution of allotetraploid cottons. Transmission genetics of G. hirsutum × G. mustelinum crosses reveals allelic interactions, constraints on fixation and selection of donor alleles, and challenges with retention of introgressed chromatin for crop improvement.

During the 2018 growing season, cotton plants in several fields in Georgia were observed with symptoms that included leaf curling, reddening and drooping of leaves, subsequent distortion of leaf growth above the nodes where reddened leaves were first observed, and shortening of upper internodes and their discoloration to deep green. These symptoms were visible in the upper portion of the plants, resembling “cotton blue” disease caused by cotton leafroll dwarf virus (CLRDV) (family Luteoviridae, genus Polerovirus). The symptoms were observed sporadically with less than 10% disease incidence within affected fields. CLRDV is a phloem-limited virus with single-stranded, positive-sense RNA genome, transmitted by aphids (Aphis gossypii) in a persistent, circulative, nonpropagative manner (Distefano et al. 2010; Sharman et al. 2015). A total of 93 symptomatic and asymptomatic leaves and petioles were collected from several different commercial cotton fields in the southern part of the state. Total RNA was extracted using the modified cetyltrimethylammonium bromide method (Sharman et al. 2015). Complementary DNA (cDNA) was synthesized from 2.5 µg of total RNA using Superscript III reverse transcription (Invitrogen, U.S.A.) and specific reverse primers targeting different open reading frames (ORFs) of the virus genome. The cDNA was used for polymerase chain reaction (PCR) with primers CLRDV3675F and Pol3982R targeting ORF 3 of the virus (310-bp product, Sharman et al. 2015) and primers 17 and 18 targeting ORF 5 (1,065-bp product, Distefano et al. 2010). A new set of primers, SB11F (5′-AGGTTTTCTGGTAGCAGTACCAATATCAACGTTA-3′) and SB11R (5′-TATCTTGCATTGTGGATTTCCCTCATAA-3′), was developed to amplify the 803-bp fragment spanning complete ORF 3 and ORF 4, encoding virus coat protein and movement protein genes. Using the three different sets of primers, products of predicted sizes were amplified from the symptomatic tissues, but not from asymptomatic tissues collected from fields and negative controls including asymptomatic leaves from plants grown in an insect-free controlled growth chamber and DNase/RNase free water (Invitrogen). Reverse transcription PCR products were gel purified, cloned into TOPO-TA cloning vector (Invitrogen), and sequenced using Sanger sequencing (GeneScript, NJ). The consensus sequence of three clones for ORF 3 and 4 from this study (MK290759 and MK290760) when analyzed using NCBI-BLASTn showed 97% sequence identity with the Brazilian and Argentinean isolates (KF906261.1 and KF359947.1, respectively) and many other isolates from South American and Asian countries. ORF 3 and 4 sequences from Georgia shared 98 to 99% identity among themselves. The partial sequences for ORF 5 (MK513938 and MK513939) shared 95% identity with the isolate from Argentina (KF359946.1 and KF359947.1). The presence of the virus was detected in all the symptomatic samples collected from 14 counties in Georgia, covering the entire cotton growing region of the state. To the best of our knowledge, this is the first report of CLRDV in Georgia, U.S.A. CLRDV infection of cotton has been reported in other cotton-growing regions in Africa, Asia, South America, and, more recently, in Alabama, U.S.A. (Avelar et al. 2018; Correa et al. 2005; Distefano et al. 2010; Mukherjee et al. 2012). With its rapid spread, this virus could pose an imminent threat and cause severe economic losses to the cotton industry. Further research is needed to elucidate epidemiology, symptomatology, vector transmission, and crop losses owing to CLRDV in the United States.

Published in Agron. J. 105:1635–1644 (2013) doi:10.2134/agronj2013.0264 Copyright © 2013 by the American Society of Agronomy, 5585 Guilford Road, Madison, WI 53711. All rights reserved. No part of this periodical may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. C is an economically important crop and provides the world’s leading natural fiber for the textile industry (Smith et al., 1999; Ulloa et al., 2007). The future of cotton improvement depends on plant characteristics conferring not only improved water-use efficiency and heat tolerance but also disease resistance. Integrating disease resistance into high-yielding, high-fiber-quality cultivars is one of the most important objectives in cotton breeding programs (Smith et al., 1999; Ulloa et al., 2009). Host-plant resistance can be a highly effective and economical approach for dealing with disease threats such as FOV and limiting yield loss in cotton (Hutmacher et al., 2011; Ulloa et al., 2010, 2011, 2013). Eight genotypes of FOV, called races, have been described (Skovgaard et al., 2001; Kim et al., 2005). Before 1986, only Races 1 and 2 were known to occur on significant acreage in the United States (DeVay, 1986). Since FOV disease in cotton was first reported in California in 1959 (Garber and Paxman, 1963), FOV Races 1 or 2 were recognized as the causal organism and were typically found in sandy soils with root-knot nematode (RKN) [Meloidogyne incognita (Kofoid and White) Chitwood] (Garber et al., 1979; Veech, 1984; Bell, 1984). The FOV fungal pathogen is a soil inhabitant that can survive for long periods in the absence of a host. Consequently, it is nearly impossible to eradicate from a field. A marked increased in the susceptibility of cultivars to FOV Race 1 was noted in the presence of RKN (Garber et al., 1979). Cotton developed for resistance to FOV on soils infested with RKN usually maintained their resistance when simultaneously challenged by both organisms, FOV Race 1 and RKN (Sasser, 1972; Heald and Orr, 1982). In 2005, University of California-Davis scientists (Kim et al., 2005) identified additional FOV races (1, 3, 4, and 8) in California soils. During the past 9 yr, FOV Race 4 has increasingly impacted cotton fields in the San Joaquin Valley (SJV) of California (Hutmacher et al., 2011). In field soils with relatively high levels of FOV Race 4, extensive disease symptoms AbStrAct During the past 9 yr, a new race of Fusarium (Fusarium oxysporum f. sp. vasinfectum [FOV Race 4]) has increasingly impacted cotton (Gossypium spp.) in the San Joaquin Valley of California. To assess the vulnerability of upland cotton (G. hirsutum L.) in California to FOV disease, elite upland germplasm lines from 13 U.S. public breeding programs across the Cotton Belt and commercial cultivars were evaluated for disease resistance to FOV Races 1 and 4. Ten independent replicated field trials were conducted: three in 2008, four in 2010, and three in 2011. Significant differences (P £ 0.05) were observed for disease severity index of leaves, vascular root staining, and plant survival values among the elite germplasm lines in all 3 yr for the levels of resistance–response to FOV Races 1 and 4. Also, significant interactions among germplasm lines, FOV races (1 and 4), and evaluation sites indicated that germplasm lines differed in mechanisms of plant-defense response for the two FOV races. Selected lines from programs in the states of Alabama, Arkansas, Louisiana, and Mississippi showed at least a moderate level of tolerance to both FOV races; however, several of these lines produced weak and coarse fibers. Based on these evaluations, many of the entries in public breeders’ current elite upland germplasm pools may be more susceptible than expected to some FOV races, and sources of acceptable levels of resistance may be limited when tested under infestation levels that resulted in only 5 to 35% plant survival in susceptible check cultivars.

A fiber length QTL, qFL-chr1, was fine mapped to a 0.9 cM interval of cotton chromosome 1. Two positional candidate genes showed positive correlation between gene expression level and fiber length. Prior analysis of a backcross-self mapping population derived from a cross between Gossypium hirsutum L. and G. barbadense L. revealed a QTL on chromosome 1 associated with increased fiber length (qFL-chr1), which was confirmed in three independent populations of near-isogenic introgression lines (NIILs). Here, a single NIIL, R01-40-08, was used to develop a large population segregating for the target region. Twenty-two PCR-based polymorphic markers used to genotype 1672 BC4F2 plants identified 432 recombinants containing breakpoints in the target region. Substitution mapping using 141 informative recombinants narrowed the position of qFL-chr1 to a 1.0-cM interval between SSR markers MUSS084 and CIR018. To exclude possible effects of non-target introgressions on fiber length, different heterozygous BC4F3 plants introgressed between SSR markers NAU3384 and CGR5144 were selected to develop sub-NILs. The qFL-chr1 was further mapped at 0.9-cM interval between MUSS422 and CIR018 by comparisons of sub-NIL phenotype, and increased fiber length by ~1 mm. The 2.38-Mb region between MUSS422 and CIR018 in G. barbadense contained 19 annotated genes. Expression levels of two of these genes, GOBAR07705 (encoding 1-aminocyclopropane-1-carboxylate synthase) and GOBAR25992 (encoding amino acid permease), were positively correlated with fiber length in a small F2 population, supporting these genes as candidates for qFL-chr1.

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.