Construction of microsatellite-based linkage map and mapping of nectarilessness and hairiness genes in Gossypium tomentosum

Gossypium tomentosum, a wild tetraploid cotton species with AD genomes, possesses genes conferring strong fibers and high heat tolerance. To effectively transfer these genes into Gossypium hirsutum, an entire microsatellite (simple sequence repeat, SSR)-based genetic map was constructed using the interspecific cross of G. hirsutum × G. tomentosum (HT). We detected 1800 loci from 1347 pairs of polymorphic primers. Of these, 1204 loci were grouped into 35 linkage groups at LOD?≥?4. The map covers 3320.8 cM, with a mean density of 2.76 cM per locus. We detected 420 common loci (186 in the At subgenome and 234 in Dt) between the HT map and the map of TM-1 (G. hirsutum) and Hai 7124 (G. barbadense; HB map). The linkage groups were assigned chromosome numbers based on location of common loci and the HB map as reference. A comparison of common markers revealed that no significant chromosomal rearrangement exist between G. tomentosum and G. barbadense. Interestingly, however, we detected numerous (33.7%) segregation loci deviating from 3:1 ratio (P?<?0.05) in HT, mostly clustering on eight chromosomes in the Dt subgenome, with some on three chromosomes in At. Two morphological traits, leaf hairiness and leaf nectarilessness were mapped on chromosomes 6 (A6) and 26 (D12), respectively. The SSR-based map constructed in this study will be useful for further genetic studies on cotton breeding, including mapping loci controlling quantitative traits associated with fiber quality, stress tolerance and developing chromosome segment specific introgression lines from G. tomentosum into G. hirsutum using marker-assisted selection.     

Genetic diversity in and phylogenetic relationships of the Brazilian endemic cotton,Gossypium mustelinum (Malvaceae)

Gossypium mustelinum, one of five tetraploid species in the cotton genus, is geographically restricted to a few states in NE Brazil. Allozyme analysis was used to assess levels and patterns of genetic diversity inG. mustelinum and its relationship to the other tetraploid species. Genetic variation was low, with only 6 of 50 loci examined being polymorphic, a mean of 1.14 alleles per locus and a mean panmictic heterozygosity of 0.08. These estimates are low relative to other tetraploid cotton species, but are typical of island endemics. Interpopulational genetic identities were uniformly high, lending support to the concept of there being only one wild species of Brazilian cotton. The limited allelic diversity observed was correlated with geographical distribution, although variability is so limited in the species that geographically marginal populations are electrophoretically ordinary. Phylogenetic and phenetic analyses demonstrate thatG. mustelinum is isolated among polyploid cotton species, occupying one of the three basal clades resulting from an early radiation of polyploid taxa subsequent to polyploid formation. We suggest thatG. mustelinum represents a paleoendemic that presently exists as a series of widely scattered, relictual populations. Despite several centuries of sympatric cultivation ofG. barbadense andG. hirsutum, there was little evidence of interspecific introgression of alleles from cultivated cottons intoG. mustelinum.     

Genetic diversity and geographic pattern in early South American cotton domestication

Amplified fragment length polymorphism fingerprinting was applied to survey the genetic diversity of primitive South American Gossypium barbadense cotton for establishing a possible link to its pre-Columbian expansion. New germplasm was collected along coastal Peru and over an Andean transect in areas where most of the archaeological evidence relating to cotton domestication has been recorded. Gene bank material of three diploid (G. raimondii, G. arboreum, and G. herbaceum) and four allotetraploid cotton species (G. hirsutum, G. mustelinum, G. tomentosum and additional G. barbadense) was added for inter- and intra-specific comparison. Eight primer combinations yielded 340 polymorphic bands among the 131 accessions. The obtained neighbor joining and unweighted pair-group method with arithmetic means are in full agreement with the known cytogenetics of the tetraploid cottons and their diploid genome donors. The four tetraploid species are clearly distinct based on taxonomic classification. The genetic diversity within G. barbadense reveals geographic patterns. The locally maintained cottons from coastal Peru display a distinct genetic diversity that mirrors their primitive agro-morphological traits. Accessions from the northernmost coast of Peru and from southwestern (SW) Ecuador cluster basal to the east-of-Andes accessions. The remaining accessions from Bolivia, Brazil, Columbia, Venezuela, and the Caribbean and Pacific islands cluster with the east-of-Andes accessions. Northwestern Peru/SW Ecuador (the area flanking the Guayaquil gulf) appears to be the center of the primitive domesticated G. barbadense cotton from where it spread over the Andes and expanded into its pre-Columbian range.This publication is dedicated to Prof. Dr. Drs.h.c. Gerhard Röbbelen on the occasion of his 75th birthday     

Gossypium tomentosum genome and interspecific ultra-dense genetic maps reveal genomic structures,recombination landscape and flowering depression in cotton

The high-quality reference-grade genome for Gossupium tomentosum can greatly promote the progress in biological research and introgression breeding for the mainly cultivated species, G. hirsutum. Here, we report a high-quality genome assembly for G. tomentosum by integrating PacBio and Hi-C technologies. Comparative genomic analysis revealed a large number of genetic variations. Two re-sequencing-based ultra-dense genetic maps were constructed which comprised 4,047,199 and 6,009,681 SNPs, 4120 and 4599 bins and covering 4126.36 cM and 4966.72 cM in the EMF₂ (F₂ from G. hirsutum × G. tomentosum) and GHF₂ (F₂ from G. hirsutum × G. barbadense). The EMF₂ exhibited lower recombination rate at the whole-genome level as compared with GHF₂. We mapped 22 and 33 QTL associated with crossover frequency and predicted Gh_MRE11 and Gh_FIGL1 as the candidate genes governing crossover in the EMF₂ and GHF₂, respectively. We identified 13 significant QTL that regulate the floral transition, and revealed that Gh_AGL18 was associated with the floral transition. Therefore, our study provides a valuable genomic resource to support a better understanding of cotton interspecific cross and recombination landscape for genetic improvement and breeding in cotton.     

Isolation, characterization and mapping of genes differentially expressed during fibre development between Gossypium hirsutum and G. barbadense by cDNA-SRAP

Gossypium hirsutum and G. barbadense are two cultivated tetraploid cotton species with differences in fibre quality. The fibre of G. barbadense is longer, stronger and finer than that of G. hirsutum. To isolate genes expressed differently between the two species during fibre development, cDNA-SRAP (sequence-related amplified polymorphism) was applied. This technique was used to analyse genes at different stages of fibre development in G. hirsutum cv. Emian22 and G. barbadense acc. 3-79, the parents of our interspecific mapping population. A total of 4096 SRAP primer combinations were used to screen polymorphism between the DNA of the parents, and 275 highly polymorphic primers were picked out to analyse DNA and RNA from leaves and fibres at different developmental stages of the parents. A total of 168 DNA fragments were isolated from gels and sequenced: 54, 30, 38 and 41 from fibres of 5, 10, 15 and 20 days post-anthesis, respectively, and five from multi stages. To genetically map these sequences, 104 sequence-specific primers were developed and were used to screened polymorphism between the mapping parents. Finally, six markers were mapped on six chromosomes of our backbone interspecific genetic map. This work can give us a primary knowledge of differences in mechanism of fibre development between G. hirsutum and G. barbadense.     

QTL analysis of leaf morphology in tetraploid Gossypium (cotton)

Molecular markers were used to map and characterize quantitative trait loci (QTLs) determining cotton leaf morphology and other traits, in 180 F₂ plants from an interspecific cross between a Gossypium hirsutum genotype carrying four morphological mutants, and a wild-type Gossypium barbadense. The prominent effects of a single region of chromosome 15, presumably the classical ”Okra-leaf” locus, were modified by QTLs on several other chromosomes affecting leaf size and shape. For most traits, each parent contained some alleles with positive effects and others with negative effects, suggesting a large potential for adapting leaf size and shape to the needs of particular production regimes. Twenty one QTLs/loci were found for the morphological traits at LOD≥3.0 and P≤0.001, among which 14 (63.6%) mapped to D-subgenome chromosomes. Forty one more possible QTLs/loci were suggested with 2.0≤LOD<3.0 and 0.001<P≤0.01. Among all of the 62 possible QTLs (found at LOD≥2.0 and P≤0.01) for the 14 morphological traits in this study, 38 (61.3%) mapped to D-subgenome chromosomes. This reinforces the findings of several other studies in suggesting that the D-subgenome of tetraploid cotton has been subject to a relatively greater rate of evolution than the A-subgenome, subsequent to polyploid formation. Received: 26 April 1999 / Accepted: 30 July 1999     

The distribution of Gossypium hirsutum chromatin in G. barbadense germ plasm: molecular analysis of introgressive plant breeding

Cotton is unusual among major crop plants in that two cross-fertile species are widely cultivated for a common economic product, fiber. Both historical evidence and classical genetic studies suggest that many improved forms of Gossypium barbadense (Sea Island, Egyptian, and Pima cottons) may include chromatin derived from G. hirsutum. Using 106 restriction fragment length polymorphism (RFLP) loci well distributed across the cotton genome, we revealed the amount and genomic distribution of G. hirsutum chromatin in 54 G. barbadense collections from around the world. The average G. barbadense collection was comprised of 8.9% alleles apparently derived from G. hirsutum. Pima cultivars (7.3 %) had fewer G. hirsutum alleles than Sea Island (9.0%) or Egyptian (9.6%) cultivars. G. hirsutum alleles were not randomly distributed, as 57.5% of the total introgression observed was accounted for by five specific chromosomal regions that span less than 10% of the genome. The average length of an introgressed chromosome segment was 12.9 cM. Overlap of introgressed chromatin in different breeding programs hints that retention of these G. hirsutum chromosomal segments may impart a selective advantage to G. barbadense genotypes. Although cluster analysis generally grouped germ plasm from common classes and/or breeding programs together, no 2 genotypes were identical — thus differences in the length and repertoire of introgressed chromosome segments also permit DNA fingerprinting of G. barbadense cultivars.     

QTL alleles for improved fiber quality from a wild Hawaiian cotton, <Emphasis Type="Italic">Gossypium tomentosum</Emphasis>

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 (P < 0.001), 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 (P < 0.001) for fiber strength and a second locus with significant genotype × environment interaction (P < 0.001) in the CA3084 background, and two loci with significant genotype × background interaction (P < 0.001) 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.     

Sampling nucleotide diversity in cotton

Background  

Cultivated cotton is an annual fiber crop derived mainly from two perennial species, Gossypium hirsutum L. or upland cotton, and G. barbadense L., extra long-staple fiber Pima or Egyptian cotton. These two cultivated species are among five allotetraploid species presumably derived monophyletically between G. arboreum and G. raimondii. Genomic-based approaches have been hindered by the limited variation within species. Yet, population-based methods are being used for genome-wide introgression of novel alleles from G. mustelinum and G. tomentosum into G. hirsutum using combinations of backcrossing, selfing, and inter-mating. Recombinant inbred line populations between genetics standards TM-1, (G. hirsutum) × 3-79 (G. barbadense) have been developed to allow high-density genetic mapping of traits.     

Molecular dissection of interspecific variation between Gossypium hirsutum and Gossypium barbadense (cotton) by a backcross-self approach: I. Fiber elongation

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 F₁ 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 BC₃F₁ plant, collectively representing G. barbadense introgression over about 70% of the genome. Twenty-four BC₃F₁ plants were selfed to generate 24 BC₃F₂ 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 (P<0.001) among-family genotype effects and genotype×family 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.Electronic Supplementary Material Supplementary material is available for this article at     

SEGREGATION IN NEW ALLOPOLYPLOIDS OF GOSSYPIUM. V. MULTIVALENT FORMATION IN NEW WORLD X ASIATIC AND NEW WORLD X WILD AMERICAN HEXAPLOIDS

The New World tetraploid cottons, G. hirsutum and G. barbadense, are natural amphidiploids (genome formula, 2[AD]) combining species of the cultivated Asiatic (2A) and wild American (2D) groups of diploid cottons. Multivalent frequency, per cell, for 2 New World X Asiatic synthetic hexaploids, G. hirsutum X G. arboreum and G. barbadense X G. arboreum, is 6.68 and 7.80, respectively. Multivalents per cell for a series of New World X wild American synthetic hexaploids are: New World X G. harknessii, 3.65;— X G. armourianum, 3.96;— X G. aridum, 3.48;— X G. lobatum, 3.66; — X G. gossypioides, 1.13. The expected correlation between multivalent frequency and genetic segregation (e.g., high multivalent frequency = high recovery of recessives, and vice versa) for these hexaploids is realized for the near-allopolyploids (New World X wild American) but only approximated for the near-autopolyploid combinations, New World X Asiatic. This is explained on the basis that different homogenetic:heterogenetic bivalent ratios are expected in autopolyploids as compared to allopolyploids.     

GENETIC DIVERSITY AND ORIGIN OF THE HAWAIIAN ISLANDS COTTON,GOSSYPIUM TOMENTOSUM

Gossypium tomentosum is the only member of the cotton genus endemic to the Hawaiian archipelago. It is morphologically distinct from other allopolyploid Gossypium species, and its phylogenetic relationships with them are uncertain. Chloroplast and ribosomal DNA restriction site variation were used to estimate the phylogeny of the allopolyploids. Gossypium mustelinum is resolved as sister to the remaining allopolyploid species, which include two species-pairs, G. barbadense-G. darwinii and G. hirsutum (including G. lanceolatum)-G. tomentosum. This indication that G. tomentosum is sister to G. hirsutum is supported by allozyme data. Gossypium tomentosum is proposed, based on biogeographic evidence and molecular data, to have originated by transoceanic dispersal from a Mesoamerican progenitor. Few restriction site variants were observed among the allopolyploids, suggesting that present lineages diverged relatively rapidly following polyploidization. Allozyme analysis of 30 G. tomentosum accessions collected from seven islands revealed relatively low levels of genetic diversity: 11 of 50 loci were polymorphic, mean number of alleles per locus was 1.24, and mean panmictic heterozygosity was 0.033. Little geographic patterning of allelic distributions was observed. Despite historical cultivation of G. barbadense and G. hirsutum in Hawaii and the existence of their naturalized derivatives, no allozyme evidence of interspecific introgression into G. tomentosum was detected.     

Some observations on photoperiodism and the development of annual forms of domesticated cottons

Observations made over the last fifteen to twenty years have discovered no primitive forms of G.barbadense L. orG. hirsutum L. (other than G.hirsutum racelatifolium Hutchinson) which are capable of flowering during the long summer days of temperate latitudes. Annual Upland cottons, grown in the southern United States since the mid-eighteenth century, were probably derived from perennial day-neutral forms of Mexican racelatifolium, though not necessarily by direct introduction from Mexico into the United States. The origin of Sea Island cottons (day-neutral forms of G.barbadense), which were formerly grown on the southeastern seaboard of the United States since the mid-eighteenth century, remains obscure. No primitive forms of this species, capable of flowering during the long summer days of temperate latitudes, have been found. An experiment is reported in which it has been possible to synthesize a day-neutral form of G.barbadense through introgression between primitive short-day sensitive forms of G.barbadense and G.hirsutum, both native to the Caribbean region. It is suggested that the ancestors of Sea Island cottons may have originated naturally by a similar mechanism involving the same species.     

Inheritance of long staple fiber quality traits of Gossypium barbadense in G. hirsutum background using CSILs

Gossypium hirsutum is a high yield cotton species that exhibits only moderate performance in fiber qualities. A promising but challenging approach to improving its phenotypes is interspecific introgression, the transfer of valuable traits or genes from the germplasm of another species such as G. barbadense, an important cultivated extra long staple cotton species. One set of chromosome segment introgression lines (CSILs) was developed, where TM-1, the genetic standard in G. hirsutum, was used as the recipient parent and the long staple cotton G. barbadense Hai7124 was used as the donor parent by molecular marker-assisted selection (MAS) in BC₅S_1–4 and BC₄S_1–3 generations. After four rounds of MAS, the CSIL population was comprised of 174 lines containing 298 introgressed segments, of which 86 (49.4%) lines had single introgressed segments. The total introgressed segment length covered 2,948.7 cM with an average length of 16.7 cM and represented 83.3% of tetraploid cotton genome. The CSILs were highly varied in major fiber qualities. By integrated analysis of data collected in four environments, a total of 43 additive quantitative trait loci (QTL) and six epistatic QTL associated with fiber qualities were detected by QTL IciMapping 3.0 and multi-QTL joint analysis. Six stable QTL were detected in various environments. The CSILs developed and the analyses presented here will enhance the understanding of the genetics of fiber qualities in long staple G. barbadense and facilitate further molecular breeding to improve fiber quality in Upland cotton.     

Bidirectional cytoplasmic and nuclear introgression in the New World cottons Gossypium barbadense and G. Hirsutum (Malvaceae)

Patterns of interspecific cytoplasmic (plastid and mitochondrial) and nuclear introgression are typically asymmetrical: cytoplasmic gene flow or “capture” is frequently observed without evidence of nuclear introgression. In contrast, nuclear introgression without concomitant cytoplasmic introgression has rarely been demonstrated. Gossypium barbadense L. and G. hirsutum L. have large indigenous ranges in the New World semiarid tropics, with an extensive area of sympatry in the Caribbean and Central America. Numerous accessions of both species were surveyed for diagnostic cpDNA restriction sites. These data, in conjunction with previous information on nuclear markers, lead to several conclusions: 1) introgression between G. hirsutum and G. barbadense is bidirectional for both nuclear and cytoplasmic genes; 2) patterns of introgression between the two species are not symmetrical—in G. barbadense, introgression of G. hirsutum alleles is largely restricted to modem cultivars and is uncommon in areas of sympatry; in contrast, introgression of G. barbadense alleles into G. hirsutum is relatively common in areas of sympatry and is rare in modem cultivars; 3) nuclear introgression is geographically more widespread and more frequently detected than cytoplasmic introgression. Several mechanisms may underlie the differential patterns of cytoplasmic and nuclear gene flow observed, including differential fitness of infraspecific and interspecific cytonuclear combinations and selection against female function in interspecific backcrosses. Possible explanations for the observed asymmetrical patterns of introgression include differences in population sizes combined with phenological differences that bias interspecific pollen transfer.     

Molecular dissection of phenotypic variation between Gossypium hirsutum and Gossypium barbadense (cotton) by a backcross-self approach: III. Fiber length

A backcross-self population from a cross between Gossypium hirsutum and G. barbadense was used to dissect the molecular basis of genetic variation governing 15 parameters that reflect fiber length. Applying a detailed restriction fragment length polymorphism (RFLP) map to 3,662 BC₃F₂ plants from 24 independently derived BC₃ families, we detected 28, nine, and eight quantitative trait loci (QTLs) for fiber length, length uniformity, and short fiber content, respectively. For eight, six, and two chromosomal regions containing quantitative trait loci (QTLs) for fiber length, length uniformity, and short fiber content (respectively), two-way analysis of variance showed a significant (P<0.001) among-family genotypic effect. A total of 13, two, and four loci showed genotype × family interaction, illustrating some of the complexities that are likely to be faced in introgression of exotic germplasm into the gene pool of cultivated cotton. Co-location of many QTLs for fiber length, length uniformity, and short fiber content accounted for correlations among these traits, while the discovery of many QTLs unique to each trait suggests that maximum genetic gain will require breeding efforts that target each trait (or an index including all three). The availability of DNA markers linked to G. barbadense QTLs identified in this and other studies promise to assist breeders in transferring and maintaining valuable traits from exotic sources during cultivar development.Electronic Supplementary Material Supplementary material is available for this article at     

Complete assignment of the chromosomes of Gossypium hirsutum L. by translocation and fluorescence in situ hybridization mapping

Significant progress has been made in the construction of genetic maps in the tetraploid cotton Gossypium hirsutum. However, six linkage groups (LGs) have still not been assigned to specific chromosomes, which is a hindrance for integrated genetic map construction. In the present research, specific bacterial artificial chromosome (BAC) clones constructed in G. hirsutum acc. TM-1 for these six LGs were identified by screening the BAC library using linkage group-specific simple-sequence repeats markers. These BAC clones were hybridized to ten translocation heterozygotes of G. hirsutum. L as BAC-fluorescence in situ hybridization probes, which allowed us to assign these six LGs A01, A02, A03, D02, D03, and D08 to chromosomes 13, 8, 11, 21, 24, and 19, respectively. Therefore, the 13 homeologous chromosome pairs have been established, and we have proposed a new chromosome nomenclature for tetraploid cotton.     

A Comparison of Leaf Anatomy in Field-grown Gossypium hirsutum and G. barbadense

Gossypium hirsutum L. (upland cotton) and G. barbadense L. (Pimacotton) are two of the most important fibre producing cottonspecies in cultivation. When grown side-by-side in the field,G.hirsutum has higher photosynthetic and transpiration rates (Luet al., 1997. Australian Journal of Plant Physiology24: 693–700).The present study was undertaken to determine if the differencesin physiology can be explained by leaf and canopy morphologyand anatomy. Scanning electron microscopy was used to comparethe leaf anatomy of field-grown upland (‘Delta’and ‘Pine Land 50’) and Pima (‘S6’)cotton. Compared to G. hirsutum, mature leaves of G. barbadenseare larger and thinner, with a thinner palisade layer. G. barbadenseleaves show significant cupping or curling which allows fora more even absorption of insolation over the course of theday and much more light penetration into the canopy. AlthoughG. barbadense leaves have a 70–78% higher stomatal densityon both the abaxial and the adaxial surfaces, its stomates areonly one third the size of those of G. hirsutum. This resultsin G. barbadense having only about 60% of the stomatal surfacearea per leaf surface area compared to G. hirsutum. These resultsare indicative of the anatomical and physiological differencesthat may limit the yield potential of G. barbadense in certaingrowing environments. Copyright 2000 Annals of Botany Company Cotton, leaf anatomy, leaf development, photosynthesis, Gossypium hirsutum, Gossypium barbadense, stomatal density     

Expansion of MIR482/2118 by a class‐II transposable element in cotton

Some plant microRNA (miRNA) families contain multiple members generating identical or highly similar mature miRNA variants. Mechanisms underlying the expansion of miRNA families remain elusive, although tandem and/or segmental duplications have been proposed. In this study of two tetraploid cottons, Gossypium hirsutum and Gossypium barbadense, and their extant diploid progenitors, Gossypium arboreum and Gossypium raimondii, we investigated the gain and loss of members of the miR482/2118 superfamily, which modulates the expression of nucleotide‐binding site leucine‐rich repeat (NBS‐LRR) disease resistance genes. We found significant expansion of MIR482/2118d in G. barbadense, G. hirsutum and G. raimondii, but not in G. arboreum. Several newly expanded MIR482/2118d loci have mutated to produce different miR482/2118 variants with altered target‐gene specificity. Based on detailed analysis of sequences flanking these MIR482/2118 loci, we found that this expansion of MIR482/2118d and its derivatives resulted from an initial capture of an MIR482/2118d by a class‐II DNA transposable element (TE) in G. raimondii prior to the tetraploidization event, followed by transposition to new genomic locations in G. barbadense, G. hirsutum and G. raimondii. The ‘GosTE’ involved in the capture and proliferation of MIR482/2118d and its derivatives belongs to the PIF/Harbinger superfamily, generating a 3‐bp target site duplication upon insertion at new locations. All orthologous MIR482/2118 loci in the two diploids were retained in the two tetraploids, but mutation(s) in miR482/2118 were observed across all four species as well as in different cultivars of both G. barbadense and G. hirsutum, suggesting a dynamic co‐evolution of miR482/2118 and its NBS‐LRR targets. Our results provide fresh insights into the mechanisms contributing to MIRNA proliferation and enrich our knowledge on TEs.