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Cotton grown in the United States are day‐length insensitive annuals and are grown under long‐day summers. Photoperiod sensitivity, present in tropical wild and landraces endemic to the center of origin and diversity, is a major barrier for the introgression of tropical gene pool into the US cotton. Previously, we mapped the major photoperiod response locus Gb_Ppd1on chromosome D06 of Pima cotton (Gossypium barbadenseL.). In the current study, an F2population of 2112 gametes was used to fine map the Gb_Ppd1locus. Two sequence‐tagged‐site and nine kompetitive allele‐specific polymerase chain reaction (KASP) markers were developed and the Gb_Ppd1locus was fine mapped to 1.1 cM region flanked by novel markers 17‐KASP‐8, 17‐KASP‐10, and 15‐PR‐10A. The closely linked markers identified 2.10 Mb region in the G. barbadensegenome that contained 18 putative gene sequences. A candidate gene Gbar_D06G014560showed high homology to VASCULAR PLANT ONE ZINC FINGER PROTEIN 1involved in photoperiodism in Arabidopsis. We evaluated the diagnostic polymorphisms for the flanking markers on a diversity panel of 91 Pima accessions. These markers would be useful in marker‐assisted selection of photoperiod response in cotton breeding. Further, quantitative gene expression analysis indicated that the CONSTANS(CO)/FLOWERING LOCUS T(FT) system is conserved in the photoperiod response pathway in Pima cotton, while COand FTare likely not the causal genes underlying flowering time at the Gb_Ppd1locus. The Gb_Ppd1gene may be an upstream regulatory sequence in the FTgene pathway that controls photoperiodism in photoperiod‐sensitive cotton by affecting the CO/FTinteraction under long‐day‐length conditions. The major effect photoperiod response locus (Gb_Ppd1) of Pima cotton was fine mapped to a 1.1 cM region flanked by new markers 15‐PR‐10A and 17‐KASP‐10.Targeted genomic mapping of Gb_Ppd1locus identified 18 putative genes in 2.10 Mb region of Gossypium barbadensegenome.Candidate gene analyses identified a homolog of VASCULAR PLANT ONE ZINC FINGER PROTEIN 1as a candidate gene for Gb_Ppd1locus.Quantitative expression analysis indicated that the CO/FTsystem in the photoperiod response pathway is likely conserved in Pima cotton, while COis likely not the causal gene at the Gb_Ppd1locus.

To incorporate root traits that improve water use efficiency (WUE) in cotton (Gossypium hirsutumL.) variety development, harnessing the genetic variability for root traits is essential. The objectives of this study were to characterize the US upland cotton core set for root traits and WUE and determine the traits associated with WUE. The core set includes 23 of the 381 accessions of the cotton diversity panel and represents 74% of the allelic diversity in US upland cotton. Plants were grown in polyvinyl chloride columns (125‐cm height, 15‐cm diameter) in a greenhouse in 2021–2022 and 2022–2023. Half of the columns contained a synthetic hardpan (1 cm thickness, 300 PSI penetration resistance) at a depth of 25 cm. Plants were harvested when >50% of the population opened bolls. Based on 16 root‐ and shoot‐traits, water use, and WUE, Deltapine 14, Station Miller, and Southland M1 were the best performers, and Toole, Paymaster HS200, Western Stormproof, CD3HCABCUH‐1‐89, and PD 2164 were the poor performers irrespective of the presence or absence of hardpan stress to root growth. The WUE of the core set genotypes was positively correlated with very fine root (diameter <0.25 mm) length, surface area, and volume and total root weight (correlation coefficient ≥0.45). These traits serve as beneficial root traits for developing new varieties with enhanced WUE. The identified genotypes and traits will be valuable for developing the next generation of water‐use‐efficient cotton varieties with a broad genetic base through advanced breeding techniques involving genomic tools and genetic diversity. The US upland cotton core set includes significant genetic variability for water use efficiency and root traits.Root weight and very fine root (diameter <0.25 mm) length, surface area, and volume improve water use efficiency.Deltapine 14, Station Miller, and Southland M1 possessed beneficial root traits and high water use efficiency.The identified root traits and genotypes would be useful resources for cotton variety development.

Cotton bacterial blight (CBB), caused by the pathogen Xanthomonas citrisubsp. malvacearum(Xcm), can inflict significant damage to cotton (Gossypium hirsutumL.) production. Previously, we identified and mapped the broad‐spectrum CBB‐resistant locus BB‐13on the long arm of chromosome D02 using array‐based single nucleotide polymorphisms (SNPs). In the current study, linked SNPs were converted into easily assayable Kompetitive Allele‐Specific PCR (KASP) markers to enable efficient detection and marker‐assisted selection of alleles at the BB‐13locus. The KASP marker's efficiency in detecting the BB‐13resistant gene was validated using an Upland cotton diversity panel of 72 accessions phenotyped with Xcmrace 18. The KASP marker NCBB‐KASP4, derived from the CottonSNP63K array‐based marker i25755Gh that is closely associated with BB‐13, predicted the CBB response phenotypes with an error rate of 4.17% in the diversity panel. Additionally, two independent biparental recombinant inbred line populations segregating for resistance to Xcmrace 18 were used for KASP marker validation and to test their utility in detecting the presence of the BB‐13locus in the resistant accession CABD3CABCH‐1‐89. NCBB‐KASP4, validated across breeding populations and broad germplasm, is a reliable KASP marker for detection and testing of BB‐13locus in cotton. Further, diagnostic array‐based SNP marker i25755Gh's allele pattern and the potential CBB response is described for 875 Gossypiumaccessions. These SNP‐based phenotypic predictions for 875 accessions along with disease response phenotypes to Xcmrace 18 for 253 accessions provide a reference for CBB resistance in diverse cotton germplasm in the United States. Linked single nucleotide polymorphisms (SNPs) converted into easily assayable Kompetitive allele‐specific PCR (KASP) markers to enable detection and marker‐assisted selection of alleles at the BB‐13locus.Validated NCBB‐KASP4 is a reliable KASP marker for detection and testing of BB‐13locus in cotton.BB‐13diagnostic KASP markers' utility was validated using a diversity panel and segregating inbred populations.SNP‐based phenotypic predictions along with cotton bacterial blight response phenotypes for diverse cotton accessions were described.

In cotton, most agronomic traits are controlled by polygenes. In this study, 110 F6recombinant inbred lines (RILs), derived from Upland cotton cross NC05AZ06 x NC11‐2100, were used to develop a linkage map and to identify quantitative trait loci (QTL) for six fiber quality traits, three yield traits, and plant height. These RILs were genotyped using the CottonSNP63K array and phenotyped for fiber quality, yield traits, and plant height in 2‐year field trials. Analysis of variance revealed significant (p< 0.05) differences among RILs for all traits studied, and the heritability estimates were moderate (30%–60%) to high (> 60%). Both positive and negative correlations were observed for fiber quality and yield traits. A total of 3,774 polymorphic SNP markers were used to develop a genetic map with an average marker density of 1.54 SNP/cM. Thirty QTL for fiber quality traits, yield traits, and plant height were detected on 15 different chromosomes, explaining 6.80%–20.02% of the phenotypic variance (PVE). Of these, 14 were major QTL (PVE > 10%), and three major QTL were detected in both years. Candidate gene analysis in the major QTL detected in both years and plant height QTL with PVE of 20.02% revealed five putative genes for fiber quality traits and one putative gene for plant height. The linkage map and identified QTL along with the candidate genes in the study could serve as additional breeding resources for Upland cotton genetic improvement. A RIL population derived from accessions with maximum allele diversity was used for QTL mapping of fiber quality and yield traits, and plant height in cotton.Broad sense heritability of the 10 agronomic traits studied ranged from moderate (30%–60%) to high (>60%) values.Thirty QTL, including 14 major QTL, of which 3 major stable QTL, were detected for fiber quality and yield traits, and plant height.

Improving fiber quality and yield are major research objectives for cotton breeders in the United States. Identifying broadly existing and stable quantitative trait loci (QTLs) related to fiber quality is critical to properly utilizing genomic resources in cotton improvement programs. An F6recombinant inbred line (RIL) population derived from the cross of NC05AZ21 × TX‐2324 was used to develop linkage maps and for QTL analysis of six fiber quality traits and lint percentage. The Illumina 63K single nucleotide polymorphism (SNP) array was used to genotype the RIL population. Analysis of variance of phenotypic trait data showed significant differences among lines and years for all traits tested. The heritability for tested traits ranged from 0.56 to 0.91. Genetic mapping was performed using 3,009 polymorphic SNP markers on the RILs. We constructed a genetic map with a total length of 4,983.73 cM and an average distance of 1.66 cM between markers. The linkage map corresponded well with the Upland cotton (Gossypium hirsutumL.) sequence‐based physical map. Thirty‐two QTLs with additive effects for lint percentage and fiber quality traits were identified on 15 chromosomes, explaining 7.9–22.2% of the phenotypic variance. The majority of these QTLs were mapped in the D subgenome, indicating that functional mutations in the D subgenome are responsible for the major fiber quality improvements in Upland cotton. Furthermore, five QTL clusters were located on four chromosomes (Chr.05, Chr.18, Chr.19, and Chr.26), which may explain the strong correlation between fiber quality traits measured. The QTLs identified in the current study could be targeted for marker‐assisted selection and map‐based cloning of fiber quality traits in Upland cotton. QTL mapping using a SNP array on a recombinant inbred line population was performed.The genetic map of SNPs corresponded well with the sequence‐based physical map.Thirty‐two QTLs for six fiber quality traits and lint percentage were identified.The D subgenome harbored the majority of QTLs for fiber quality in Upland cotton.QTLs for fiber quality traits clustered on a handful of chromosomal regions.

Two conventional upland cotton (Gossypium hirsutumL.) germplasm lines, NC18‐05 (Reg. no. GP‐1082, PI 697272) and NC18‐06 (Reg. no. GP‐1083, PI 697273), were developed by the Department of Crop and Soil Sciences at North Carolina State University. The lines were bred for fiber elongation within yield‐competitive phenotypes. The two lines were derived from a randomly mated population using multiple parental lines. Both NC18‐05 and NC18‐06 produced equivalent or higher lint than commercial cultivars ‘DP393’, ‘SG747’, and ‘UA48’ during 2 yr in Clayton, NC. Germplasm line NC18‐05 produced 1507.2 kg ha–1of lint, which was 36.2% higher than DP393 and 29.4% higher than UA48 (p< .05). Germplasm line NC18‐06 produced 1428.6 kg ha–1of lint, which was 29.1% higher than DP393 and 22.6% higher than UA48 (p< .05). However, neither line yielded more lint per hectare than SG747 or the average of the parental lines (p> .05). Both NC18‐05 and NC18‐06 exhibited equal or higher fiber elongation values (6.0–49.2%) than the commercial cultivar controls. These two lines had higher lint percentages than UA48 (p< .05). NC18‐06 also demonstrated stronger fiber than DP393 and SG747 (p< .05). These two germplasm lines offer breeders a new source of exceptional fiber elongation before break within a high‐yielding background.

In its natural state, cotton (Gossypiumspp.) is a perennial that flowers only under short‐day conditions. Early selection efforts eliminated this photoperiod requirement, allowing cotton cultivation to shift predominantly to annual growth under long summer daylengths throughout the world. Photoperiod sensitivity persists in many wild cottons and remains a major barrier to the introgression of beneficial alleles into elite breeding material. Identification of the variation and genetic factors underlying photoperiod response in cotton is needed to fully harness the genetic diversity of wild cotton and broaden the cultivated germplasm pool. Genetic variants, especially loss‐of‐function mutations in dominant genes conferring photoperiod sensitivity, would be highly valuable in this regard. After mutagenizing pima cotton (G. barbadenseL.) seeds heterozygous for the major photoperiod response gene Gb_Ppd1with γ rays, we identified plants no longer sensitive to photoperiod. Genetic analysis of BC1F1plants derived from backcrossing the mutants with their photoperiod‐insensitive parent confirmed the loss‐of‐function mutations were allelic with Gb_Ppd1. Characterization of the mutants with molecular markers confirmed that all but one were deletions of Gb_Ppd1. Further, genotyping localized Gb_Ppd1to a 12‐Mb region on chromosome D10. The newly identified genomic region and loss‐of‐function mutants may help assist with the identification and functional validation of candidate genes for photoperiod response in cotton, facilitating the valuable introgression of genetic diversity into cotton breeding programs.

Four upland cotton (Gossypium hirsutumL.) germplasm lines, NC18‐11 (Reg. no. GP‐1056, PI 690771), NC18‐12 (Reg. no. GP‐1057, PI 690772), NC18‐13 (Reg. no. GP‐1058, PI 690773), and NC18‐14 (Reg. no. GP‐1059, PI 690774), were developed by the Department of Crop and Soil Sciences at North Carolina State University. These four cotton lines had improved fiber quality traits and exhibited 915.5 to 1180.9 kg ha−1lint yield. All four lines were derived from a random mated population using multiple parental lines. The four lines were compared with commercial cultivars ‘DP393’, ‘Sure‐Grow 747’, and ‘UA48’ over 2 yr using a replicated randomized complete block design in Clayton, NC. Lines NC18‐11, NC18‐12, and NC18‐13 had significantly (p= 0.05) better micronaire values than the checks and significantly higher strength values (8.3–25.3%) than DP393, Sure‐Grow 747, and the parental lines. These three lines also had significantly (p= 0.05) greater upper half mean length values (4.9–11.6%) than DP393 and Sure‐Grow 747. Germplasm line NC18‐14 had a 15.4 to 62.5% significantly (p= 0.05) higher fiber elongation value than all checks and parental lines and showed 5.0 to 12.8% more lint fraction than the checks. These lines could be additional sources of genetic variability for cotton breeding programs focusing on improving fiber quality traits while still producing more than 900 kg ha−1of lint.

Four upland cotton (Gossypium hirsutumL.) lines, NC18‐07 (Reg. no. GP‐1052, PI 690767), NC18‐08 (Reg. no. GP‐1053, PI 690768), NC18‐09 (Reg. no. GP‐1054, PI 690769), and NC18‐10 (Reg. no. GP‐1055, PI 690770), were developed by the Department of Crop and Soil Sciences at North Carolina State University. The four upland cotton lines have improved yield production and some good fiber quality traits. All four lines were derived from a random mated population using multiple parental lines. These four lines were compared with commercial check cultivars ‘DP393’, ‘Sure‐Grow 747’, and ‘UA48’ over 2 yr in Clayton, NC. NC18‐07 produced 7.6 to 34.2% greater lint yields than that of the checks and had 15.2% greater elongation value than that of UA48. NC18‐08 produced 5.9 to 32.1% greater lint yield than the checks. NC18‐09 yielded 2.2 to 27.5% greater lint than checks and showed 44.7 and 22.3% greater elongation values than that of UA48 and parental lines, respectively. Germplasm line NC18‐10 produced 1.0 to 26.0% greater lint yield than the commercial checks and also displayed 26.5 and 7.0% greater elongation values than that of UA48 and parental lines, respectively. These lines could be valuable sources for cotton breeding and programs focusing on improving yield as well as fiber elongation.

Three hundred and ninety-one Gossypium hirsutumand 34 Gossypium barbadenseaccessions were screened for thrips resistance under field conditions at the Upper Coastal Plain Research Station in Rocky Mount, North Carolina in years 2014 and 2015. Visual damage ratings, thrips counts, and seedling dry weights were recorded at 2.5, 3.5, and 4.5 wk after planting, respectively. Population density and thrips arrival times varied between years. Data from the three separate damage scoring dates provided a better estimate of resistance or susceptibility to thrips than ratings from the individual dates over the season. Tobacco thrips [Frankliniella fusca(Hinds) (Thysanoptera: Thripidae)], followed by western flower thrips [Frankliniella occidentalis(Pergande) (Thysanoptera: Thripidae)], were the dominant thrips species observed in the study. Five resistant G. barbadenseaccessions and five moderately resistant upland cotton accessions were identified from field evaluations. Greenhouse experiments were conducted in Fall 2015 and Spring 2016 to determine if plant height, growth rate, leaf pubescence, and leaf area were significantly different in resistant and susceptible groups of G. hirsutumand G. barbadenseaccessions identified from the field screenings. Leaf pubescence and relative growth rate were significantly higher in resistant accessions compared with susceptible accessions in absence of thrips. There was no difference for plant height and leaf area between resistant and susceptible groups. Results suggest thrips-resistant plants have a possible competitive advantage through faster growth and higher trichome density, which limits thrips movement.

In this study, genetic diversity and population structure was assessed in a set of 185 Gossypium hirsutumL. landrace accessions, collected mainly from Central America during the mid‐1900s using genomewide simple sequence repeat (SSR) markers. Genotyping the diversity panel using 122 SSRs detected 143 marker loci. A total of 819 alleles were identified across 143 markers loci, and out of these, 23.3% were unique alleles, observed only in one accession. Average genetic distance between accessions was 0.36, suggesting higher levels of genetic variation present in the cotton tropical landrace germplasm. Using Bayesian model‐based structure analysis, five major subgroups were identified that roughly corresponded to the geographical origins of accessions. Substantial admixture was observed as accessions from different geographical locations were grouped together. Results from phylogenetic analysis, principal component analysis, and analysis of molecular variance supported clustering based on STRUCTURE analysis. Pairwise kinship estimates suggested that most of the accessions were unrelated. Finally, core sets representing various levels of allelic richness were identified using POWERMARKER. Assessing genetic diversity, population structure, and identifying the core sets in the landraces will facilitate the utilization of unexploited tropical genetic diversity towards developing improved cotton cultivars.

Gossypium arboreumL, which produces spinnable cotton fibers, is an A‐genome diploid progenitor species of tetraploid cotton. With its diploid genome, publicly available genome sequence, adapted growth, and developmental and agronomic attributes, G. arboreumcould make an ideal cotton species to study the genetic basis of biological traits that are controlled by orthologous loci in diploid and polyploid species. Leaf shape is an important agronomic trait in cotton. Normal, subokra, okra, and laciniate are the predominant leaf shapes in cotton cultivars. Laciniate in diploids is phenotypically similar to okra leaf shape in tetraploid. In the present study, a population of 135 F2plants derived from accessions NC 501 and NC 505 was used for genetic and molecular mapping of laciniate leaf shape in diploid cotton (G. arboreum). An inheritance study showed that laciniate leaf shape was controlled by a single incompletely dominant gene (LL–A2). Molecular genetic mapping using simple‐sequence repeat (SSR) markers placed the leaf shape locus L‐A2on chromosome 2. Targeted mapping using putative genes from the delineated region established that laciniate leaf shape in G. arboreumand okra leaf shape in Gossypium hirsutumL. were controlled by genes at orthologous loci. Collinearity was well conserved between the diploid A‐ (G. arboreum) and D‐ (G. raimondiiUlbr.) genomes in the targeted genomic region narrowing the candidate region for the leaf shape locus (L‐A2) to nine putative genes. Establishing the orthologous genomic region for the Lloci could help use the diploid cotton resources toward map‐based cloning of leaf shape genes in Gossypium.

Photoperiod sensitivity is a major barrier to using introgressions from the tropical gene pool in cotton breeding programs in North America. To better understand the genetic processes underlying photoperiod response in Pima cotton, a photoperiod‐insensitive line, Pima S‐7, was crossed to a photoperiod‐sensitive landrace accession, NC7018. An F2mapping population of 211 individuals was used to establish that a single dominant gene controls the photoperiod sensitivity in Gossypium barbadense. Molecular mapping with simple sequence repeat (SSR) markers localized the photoperiod response gene Gb_Ppd1to a 3.3‐cM region on chromosome 25 of the Pima cotton genetic map. Orthologous mapping of the flanking markers with the draft diploid D‐genome sequence resolved the photoperiod response gene to a 5.8 Mb region close to the centromere on chromosome 10 of Gossypium raimondii. In silico mapping of the flowering‐time candidate genes of model plant species suggested that the putative gene Gorai.010G161200of G. raimondii, which has a function involved in photoperiodism, was mapped in the genomic region of Gb_Ppd1. Identification of closely linked molecular markers and the delineated genomic region in sequenced G. raimondiigenome will aid marker‐assisted selection and molecular isolation of photoperiod response loci in cotton.

During the past 9 yr, a new race of Fusarium(Fusarium oxysporumf. sp. vasinfectum[FOV Race 4]) has increasingly impacted cotton (Gossypiumspp.) in the San Joaquin Valley of California. To assess the vulnerability of upland cotton (G. hirsutumL.) 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.

NC05AZ21 (Reg. No. GP‐966, PI 667659) is an okra‐leaf line and NC05‐11 (Reg. No., GP‐965, PI 667658) is a normal‐leaf line of Upland cotton (Gossypium hirsutumL.). NC05AZ21 was developed from a cross of NC 72 and an unknown okra leaf, red stem line from Louisiana while NC05‐11 was developed from a cross of NC 72 and Fiber Max 989 (FM 989). NC 72 is a normal and smooth leaf line. FM 989 is a commercial, normal‐leaf cultivar. A pedigree breeding method was followed in developing these lines. Both lines were compared with two commercial cultivars across multiple environments for agronomic traits. Line NC05AZ21 was also compared with a commercial okra‐leaf cultivar FM 832 for agronomic performance. NC05AZ21 showed superior lint yield and lint percentage to and comparable fiber length as FM 832. It had a lower lint yield but longer fibers than Deltapine 455BG/RR (DP 455BG/RR) and Stoneville 5327B2RF (ST 5327B2RF) and comparable fiber strength. It has good resistance to Fusarium wilt [caused by Fusarium oxysporumSchlet.f.sp. vasinfectum(Atk.) Snyd. &Hans.] as well. It could be a good source of earliness and Fusarium wilt resistance and perhaps tolerance to boll rot (caused by numerous organisms)—the latter because of its okra‐leaf shape. NC05‐11 had comparable lint yields as DP 451BG/RR and DP 455BG/RR with superior fiber length and strength. It also had good resistance to Fusarium wilt. Both NC05AZ21 and NC05‐11 could prove to be valuable sources of additional genetic variability for cotton breeding programs having an emphasis on improving Fusarium wilt resistance and fiber quality.

The wheat (Triticum aestivumL.)‐Aegilops geniculataintrogression T5DL·5DS‐5MgS(0.95), with stripe rust resistance gene Yr40and leaf rust resistance gene Lr57, is an effective source of resistance against most isolates of the rust pathogen in Kansas and India. Rust resistance genes Lr57and Yr40were transferred to the hard red winter wheat (HRWW) cultivars Jagger and Overley by standard backcrossing and marker‐assisted selection (MAS). PCR‐based cleaved amplified polymorphic sequence (CAPS) markers were developed and used to select backcross F1plants with rust resistance. Diagnostic polymorphism detected by CAPS marker XLr57/Yr40‐MAS‐CAPS16 was consistent between the resistant source and a set of wheat cultivars selected by the U.S. Wheat Coordinated Agricultural Project. Homozygous BC3F2plants with rust resistance genes were selected using the Restriction Fragment Length Polymorphisms (RFLP)‐based diagnostic DNA marker polymorphism detected by the wheat grain softness protein (GSP). Deletion of Puroindoline a (Pina‐Mg1) and Puroindoline b (Pinb‐Mg1) gene sequences in the chromosome segment of 5MgS substituting for 5DS of wheat suggests that the backcross derivatives with Lr57/Yr40can be used to develop hard textured wheats. The HRWW germplasm with Lr57and Yr40will provide breeders in the Southern Great Plains with adapted lines having an additional source of resistance that can be used to achieve durability of rust resistance.

Genes transferred to crop plants from wild species are often associated with deleterious traits. Using molecular markers, we detected a cryptic introgression with a leaf rust resistance gene transferred from Aegilops triuncialisL. into common wheat (Triticum aestivumL.). One agronomically desirable rust‐resistant introgression line was selected and advanced to BC3F11from a cross of hexaploid wheat and A. triuncialisIn situ hybridization using A. triuncialisgenomic DNA as a probe failed to detect the alien introgression. The translocation line was resistant to the most prevalent races of leaf rust in India and Kansas. Genetic mapping in a segregating F2:3population showed that the rust resistance was monogenically inherited. Homeologous group 2 restriction fragment length polymorphism markers XksuF11, XksuH16, and Xbg123showed diagnostically polymorphic alleles between the resistant and susceptible bulks. The alien transfer originated from homeologous chromosome recombination. The A. triuncialis‐specific alleles of XksuH16, XksuF11, Xbg123, and one simple sequence repeat marker Xcfd50cosegregated with the rust resistance, suggesting that the wheat–A. triuncialistranslocation occurred in the distal region of chromosome arm 2BL. This translocation was designated T2BS·2BL‐2tL(0.95). The unique source and map location of the introgression on chromosome 2B indicated that the leaf rust resistance gene is new and was designated Lr58

Seed color is an important trait affecting flour yield and quality in wheat. Seed color also is either tightly linked to or pleiotropically controls seed dormancy in wheat, because most of the red‐seeded wheats are tolerant to preharvest sprouting in comparison to white‐seeded wheats. Seed color in hexaploid wheat is controlled by the dominant red seed color genes R‐A1, R‐B1, and R‐D1located in orthologous positions on chromosome arms 3AL, 3BL, and 3DL, respectively. By using wheat ESTs and synteny with rice, we identified one STS marker and one EST marker flanking R‐A1in a 4.4‐cM interval by using an RIL and F2populations of Langdon (LDN)/LDN‐DIC3A (disomic substitution of T. turgidumsubsp. dicoccoideschromosome 3A for 3A of LDN). Physical mapping of the R‐A1gene using tightly linked markers on a set of deletion lines specific to the long arms of group‐3 chromosomes indicated that the red seed color genes are located in the distal region (less than 10% of the chromosome arm 3L), which is a high‐recombination, gene‐rich region in wheat. Comparative genomic analysis indicated that, except for a very minor rearrangement of gene sequences in wheat relative to rice, macrocolinearity is well conserved between the consensus distal deletion bin of wheat 3L‐0.80–1.00 and rice chromosome arm 1L. The R‐A1gene of wheat was targeted into a single PAC of rice using colinear flanking markers.