Construction of a complete set of alien chromosome addition lines from Gossypium australe in Gossypium hirsutum: morphological, cytological, and genotypic characterization

Identification of chromosomes by fluorescence in situ hybridization in Gossypium hirsutum via developing oligonucleotide probes

Discrimination of chromosome is essential for chromosome manipulation or visual chromosome characterization. Oligonucleotide probes can be employed to simplify the procedures of chromosome identification in molecular cytogenetics due to its simplicity, fastness, cost-effectiveness, and high efficiency. So far, however, visual identification of cotton chromosomes remains unsolved. Here, we developed 16 oligonucleotide probes for rapid and accurate identification of chromosomes in Gossypium hirsutum: 9 probes, of which each is able to distinguish individually one pair of chromosomes, and seven probes, of which each distinguishes multiple pairs of chromosomes. Besides the identification of Chrs. A09 and D09, we first find Chr. D08, which carries both 45S and 5S rDNA sequences. Interestingly, we also find Chr. A07 has a small 45S rDNA size, suggesting that the size of this site on Chr. A07 may have reduced during evolution. By the combination of 45S and 5S rDNA sequences and oligonucleotide probes developed, 10 chromosomes (Chrs. 3-7, and 9-13) in A subgenome and 7 (Chrs. 1-2, 4-5, and 7-9) in D subgenome of cotton are able to be recognized. This study establishes cotton oligonucleotide fluorescence in situ hybridization technology for discrimination of chromosomes, which supports and guides for sequence assembling, particularly, for tandem repeat sequences in cotton.

Genomic and Cytogenetic Analysis of Synthetic Polyploids between Diploid and Tetraploid Cotton (Gossypium) Species

Cotton (Gossypium spp.) is the most important natural fiber source in the world. The genetic potential of cotton can be successfully and efficiently exploited by identifying and solving the complex fundamental problems of systematics, evolution, and phylogeny, based on interspecific hybridization of cotton. This study describes the results of interspecific hybridization of G. herbaceum L. (A1-genome) and G. mustelinum Miers ex Watt (AD4-genome) species, obtaining fertile hybrids through synthetic polyploidization of otherwise sterile triploid forms with colchicine (C22H25NO6) treatment. The fertile F1C hybrids were produced from five different cross combinations: (1) G. herbaceum subsp. frutescens × G. mustelinum; (2) G. herbaceum subsp. pseudoarboreum × G. mustelinum; (3) G. herbaceum subsp. pseudoarboreum f. harga × G. mustelinum; (4) G. herbaceum subsp. africanum × G. mustelinum; (5) G. herbaceum subsp. euherbaceum (variety A-833) × G. mustelinum. Cytogenetic analysis discovered normal conjugation of bivalent chromosomes in addition to univalent, open, and closed ring-shaped quadrivalent chromosomes at the stage of metaphase I in the F1C and F2C hybrids. The setting of hybrid bolls obtained as a result of these crosses ranged from 13.8-92.2%, the fertility of seeds in hybrid bolls from 9.7-16.3%, and the pollen viability rates from 36.6-63.8%. Two transgressive plants with long fiber of 35.1-37.0 mm and one plant with extra-long fiber of 39.1-41.0 mm were identified in the F2C progeny of G. herbaceum subsp. frutescens × G. mustelinum cross. Phylogenetic analysis with 72 SSR markers that detect genomic changes showed that tetraploid hybrids derived from the G. herbaceum × G. mustelinum were closer to the species G. mustelinum. The G. herbaceum subsp. frutescens was closer to the cultivated form, and its subsp. africanum was closer to the wild form. New knowledge of the interspecific hybridization and synthetic polyploidization was developed for understanding the genetic mechanisms of the evolution of tetraploid cotton during speciation. The synthetic polyploids of cotton obtained in this study would provide beneficial genes for developing new cotton varieties of the G. hirsutum species, with high-quality cotton fiber and strong tolerance to biotic or abiotic stress. In particular, the introduction of these polyploids to conventional and molecular breeding can serve as a bridge of transferring valuable genes related to high-quality fiber and stress tolerance from different cotton species to the new cultivars.

RVE2, a new regulatory factor in jasmonic acid pathway, orchestrates resistance to Verticillium wilt

Verticillium dahliae, one of the most destructive fungal pathogens of several crops, challenges the sustainability of cotton productivity worldwide because very few widely-cultivated Upland cotton varieties are resistant to Verticillium wilt (VW). Here, we report that REVEILLE2 (RVE2), the Myb-like transcription factor, confers the novel function in resistance to VW by regulating the jasmonic acid (JA) pathway in cotton. RVE2 expression was essentially required for the activation of JA-mediated disease-resistance response. RVE2 physically interacted with TPL/TPRs and disturbed JAZ proteins to recruit TPL and TPR1 in NINJA-dependent manner, which regulated JA response by relieving inhibited-MYC2 activity. The MYC2 then bound to RVE2 promoter for the activation of its transcription, forming feedback loop. Interestingly, a unique truncated RVE2 widely existing in D-subgenome (GhRVE2D) of natural Upland cotton represses the ability of the MYC2 to activate GhRVE2A promoter but not GausRVE2 or GbRVE2. The result could partially explain why Gossypium barbadense popularly shows higher resistance than Gossypium hirsutum. Furthermore, disturbing the JA-signalling pathway resulted into the loss of RVE2-mediated disease-resistance in various plants (Arabidopsis, tobacco and cotton). RVE2 overexpression significantly enhanced the resistance to VW. Collectively, we conclude that RVE2, a new regulatory factor, plays a pivotal role in fine-tuning JA-signalling, which would improve our understanding the mechanisms underlying the resistance to VW.

Rapid and visual monitoring of alien sequences using crop wild relatives specific oligo-painting: The case of cucumber chromosome engineering

Wild species related to domesticated crops (crop wild relatives, or CWRs) represent a high level of genetic diversity that provides a practical gene pool for crop pre-breeding employed to address climate change and food demand challenges globally. Nevertheless, rapid identifying and visual tracking of alien chromosomes and sequences derived from CWRs have been a technical challenge for crop chromosome engineering. Here, a species-specific oligonucleotide (oligo) pool was developed by using the reference genome of Cucumis hystrix (HH, 2n = 2x = 24), a wild species carrying many favorable traits and interspecific compatibility with cultivated cucumber (C. sativus, CC, 2n = 2x = 14). These synthetic double-stranded oligo probes were applied to validate the assembly and characterize the chromosome architectures of C. hystrix, as well as to rapidly identify C. hystrix-chromosomes in diverse C. sativus-hystrix chromosome-engineered germplasms, including interspecific hybrid F1 (HC), synthetic allopolyploids (HHCC, CHC, and HCH) and alien additional lines (CC-H). Moreover, a ∼2Mb of C. hystrix-specific sequences, introduced into cultivated cucumber, were visualized by CWR-specific oligo-painting. These results demonstrate that the CWR-specific oligo-painting technique holds broad applicability for chromosome engineering of numerous crops, as it allows rapid identification of alien chromosomes, reliable detection of homoeologous recombination, and visual tracking of the introgression process. It is promising to achieve directed and high-precision crop pre-breeding combined with other breeding techniques, such as CRISPR/Cas9-mediated chromosome engineering.

A comprehensive molecular cytogenetic analysis of the genome architecture in modern sugarcane cultivars

Modern sugarcane cultivars are derived from the hybridization of Saccharum officinarum (2n = 80) and S. spontaneum (2n = 40-128), leading to a variety of complex genomes with highly polyploid and varied chromosome structures. These complex genomes have hindered deciphering the genome structure and marker-assisted selection in sugarcane breeding. Ten cultivars were analyzed by fluorescence in situ hybridization adopting chromosome painting and S. spontaneum-specific probes. The results showed six types of chromosomes in the studied cultivars, including S. spontaneum or S. officinarum chromosomes, interspecific recombinations from homoeologous or nonhomoeologous chromosomes, and translocations of S. spontaneum or S. officinarum chromosomes. The results showed unexpectedly high proportions of interspecific recombinations in these cultivars (11.9-40.9%), which renew our knowledge that less than 13% of chromosomes result from interspecific exchanges. Also, the results showed a high frequency of translocations (an average of 2.15 translocations per chromosome) between S. officinarum chromosomes. The diverse types of chromosomes in cultivars imply that hybrid gametes of S. spontaneum and S. officinarum may form unusual chromosome pairs, including homoeologous or nonhomoeologous chromosomes either between or within S. spontaneum and S. officinarum. Moreover, we consistently observed 11 or 12 copies for the four studied chromosomes, i.e., chromosomes 1, 2, 7, and 8, suggesting steady transmission during the breeding program. By comparison, we found a relatively fewer copies of S. spontaneum chromosome 1 than those of S. spontaneum chromosomes 2, 7, and 8. These results provide deep insights into the structure of cultivars and may facilitate chromosome-assisted selection in sugarcane breeding.

Understanding and exploiting uniparental genome elimination in plants: insights from Arabidopsis thaliana

Uniparental genome elimination (UGE) refers to the preferential exclusion of one set of the parental chromosome complement during embryogenesis following successful fertilization, giving rise to uniparental haploid progeny. This artificially induced phenomenon was documented as one of the consequences of distant (wide) hybridization in plants. Ten decades since its discovery, attempts to unravel the molecular mechanism behind this process remained elusive due to a lack of genetic tools and genomic resources in the species exhibiting UGE. Hence, its successful adoption in agronomic crops for in planta (in vivo) haploid production remains implausible. Recently, Arabidopsis thaliana has emerged as a model system to unravel the molecular basis of UGE. It is now possible to simulate the genetic consequences of distant crosses in an A. thaliana intraspecific cross by a simple modification of centromeres, via the manipulation of the centromere-specific histone H3 variant gene, CENH3. Thus, the experimental advantages conferred by A. thaliana have been used to elucidate and exploit the benefits of UGE in crop breeding. In this review, we discuss developments and prospects of CENH3 gene-mediated UGE and other in planta haploid induction strategies to illustrate its potential in expediting plant breeding and genetics in A. thaliana and other model plants.

Morphological description of a novel synthetic allotetraploid(A1A1G3G3) of Gossypium herbaceum L.and G.nelsonii Fryx. suitable for disease-resistant breeding applications

Wild species of Gossypium ssp. are an important source of traits for improving commercial cotton cultivars. Previous reports show that Gossypium herbaceum L. and Gossypium nelsonii Fryx. have better disease resistance characteristics than commercial cotton varieties. However, chromosome ploidy and biological isolation make it difficult to hybridize diploid species with the tetraploid Gossypium hirsutum L. We developed a new allotetraploid cotton genotype (A1A1G3G3) using a process of distant hybridization within wild cotton species to create new germplasms. First of all, G. herbaceum and G. nelsonii were used for interspecific hybridization to obtain F1 generation. Afterwards, apical meristems of the F1 diploid cotton plants were treated with colchicine to induce chromosome doubling. The new interspecific F1 hybrid and S1 cotton plants originated from chromosome duplication, were tested via morphological and molecular markers and confirmed their tetraploidy through flowrometric and cytological identification. The S1 tetraploid cotton plants was crossed with a TM-1 line and fertile hybrid offspring were obtained. These S2 offsprings were tested for resistance to Verticillium wilt and demonstrated adequate tolerance to this fungi. The results shows that the new S1 cotton line could be used as parental material for hybridization with G. hirsutum to produce pathogen-resistant cotton hybrids. This new S1 allotetraploid genotype will contributes to the enrichment of Gossypium germplasm resources and is expected to be valuable in polyploidy evolutionary studies.

Development of alien addition lines from Cucumis hystrix in Cucumis sativus: cytological and molecular marker analyses

Transferring desired genes from wild species to cultivars through alien addition lines (AALs) has been shown to be an effective method for genetic improvement. Cucumis hystrix Chakr. (HH, 2n = 24) is a wild species of Cucumis that possesses many resistant genes. A synthetic allotetraploid species, C. hytivus (HHCC, 2n = 38), was obtained from the cross between cultivated cucumber, C. sativus (CC, 2n = 14), and C. hystrix followed by chromosome doubling. Cucumis sativus - C. hystrix AALs were developed by continuous backcrossing to the cultivated cucumbers. In this study, 10 different types of AALs (CC-H01, CC-H06, CC-H08, CC-H10, CC-H12, CC-H06+H09, CC-H06+H10, CC-H06+H12, CC-H08+H10, CC-H01+H06+H10) were identified based on the analysis of fluorescence in situ hybridization (FISH) and molecular markers specific to C. hystrix chromosomes. And the behavior of the alien chromosomes in three AALs (CC-H01, CC-H06+H10, CC-H01+H06+H10) at meiosis was investigated. The results showed that alien chromosomes paired with C. sativus chromosome in few pollen mother cells (PMCs). Further, disomic alien addition lines (DAALs) carrying a pair of C. hystrix chromosome H10 were screened from the selfed progenies of CC-H10. Chromosome pairing between genomes provides cytological evidence for the possible introgression of alien chromosome segments. The development of AALs could serve as a key step for exploiting and utilizing valuable genes from C. hystrix.

A complete set of monosomic alien addition lines developed from Gossypium anomalum in a Gossypium hirsutum background: genotypic and phenotypic characterization

Gossypium anomalum (B₁B₁) is a valuable wild resource for the genetic improvement of G. hirsutum (A₁A₁D₁D₁) in terms of fiber quality and disease and pest resistance, but the inherent difficulties in distant hybridization hinder its utilization in breeding programs. Monosomic alien addition lines (MAALs) are powerful tools for interspecific gene transfer. First, to access useful genes from G. anomalum, a fertile hexaploid from G. hirsutum × G. anomalum was obtained and then additional chromosomes were selected using SSR markers in successive backcrosses and self-crossing from BC₂F₁ to BC₄F₄. Finally, a complete set of 13 MAALs were developed. All the MAALs were confirmed by chromosome-specific anchored SSRs and genome-wide resequencing. The MAALs demonstrated abundant variation in morphological, agronomic, yield-related, and fiber quality traits. MAAL_3B had excellent fiber strength and fineness, indicating that the transmitted chromosome may carry desirable genes for the observed phenotypes. This complete set of MAALs will provide important genetic bridge material for the identification and introgression of favorable genes from G. anomalum and lay an important foundation for the genetic improvement of cotton.

Genome sequencing of the Australian wild diploid species Gossypium australe highlights disease resistance and delayed gland morphogenesis

The diploid wild cotton species Gossypium australe possesses excellent traits including resistance to disease and delayed gland morphogenesis, and has been successfully used for distant breeding programmes to incorporate disease resistance traits into domesticated cotton. Here, we sequenced the G. australe genome by integrating PacBio, Illumina short read, BioNano (DLS) and Hi-C technologies, and acquired a high-quality reference genome with a contig N50 of 1.83 Mb and a scaffold N50 of 143.60 Mb. We found that 73.5% of the G. australe genome is composed of various repeat sequences, differing from those of G. arboreum (85.39%), G. hirsutum (69.86%) and G. barbadense (69.83%). The G. australe genome showed closer collinear relationships with the genome of G. arboreum than G. raimondii and has undergone less extensive genome reorganization than the G. arboreum genome. Selection signature and transcriptomics analyses implicated multiple genes in disease resistance responses, including GauCCD7 and GauCBP1, and experiments revealed induction of both genes by Verticillium dahliae and by the plant hormones strigolactone (GR24), salicylic acid (SA) and methyl jasmonate (MeJA). Experiments using a Verticillium-resistant domesticated G. barbadense cultivar confirmed that knockdown of the homologues of these genes caused a significant reduction in resistance against Verticillium dahliae. Moreover, knockdown of a newly identified gland-associated gene GauGRAS1 caused a glandless phenotype in partial tissues using G. australe. The G. australe genome represents a valuable resource for cotton research and distant relative breeding as well as for understanding the evolutionary history of crop genomes.

Field cress genome mapping: Integrating linkage and comparative maps with cytogenetic analysis for rDNA carrying chromosomes

Field cress (Lepidium campestre L.), despite its potential as a sustainable alternative oilseed plant, has been underutilized, and no prior attempts to characterize the genome at the genetic or molecular cytogenetic level have been conducted. Genetic maps are the foundation for anchoring and orienting annotated genome assemblies and positional cloning of candidate genes. Our principal goal was to construct a genetic map using integrated approaches of genetic, comparative and cytogenetic map analyses. In total, 503 F2 interspecific hybrid individuals were genotyped using 7,624 single nucleotide polymorphism markers. Comparative analysis demonstrated that ~57% of the sequenced loci in L. campestre were congruent with Arabidopsis thaliana (L.) genome and suggested a novel karyotype, which predates the ancestral crucifer karyotype. Aceto-orcein chromosome staining and fluorescence in situ hybridization (FISH) analyses confirmed that L. campestre, L. heterophyllum Benth. and their hybrids had a chromosome number of 2n = 2x = 16. Flow cytometric analysis revealed that both species possess 2C roughly 0.4 picogram DNA. Integrating linkage and comparative maps with cytogenetic map analyses assigned two linkage groups to their particular chromosomes. Future work could incorporate FISH utilizing A. thaliana mapped BAC clones to allow the chromosomes of field cress to be identified reliably.

Transcriptional and epigenetic adaptation of maize chromosomes in Oat-Maize addition lines

By putting heterologous genomic regulatory systems into contact, chromosome addition lines derived from interspecific or intergeneric crosses allow the investigation of transcriptional regulation in new genomic environments. Here, we report the transcriptional and epigenetic adaptation of stably inherited alien maize chromosomes in two oat–maize addition (OMA) lines. We found that the majority of maize genes displayed maize-specific transcription in the oat genomic environment. Nevertheless, a quarter of the expressed genes encoded by the two maize chromosomes were differentially expressed genes (DEGs). Notably, highly conserved orthologs were more severely differentially expressed in OMAs than less conserved orthologs. Additionally, syntenic genes and highly abundant genes were over-represented among DEGs. Gene suppression was more common than activation among the DEGs; however, the genes in the former maize pericentromere, which expanded to become the new centromere in OMAs, were activated. Histone modifications (H3K4me3, H3K9ac and H3K27me3) were consistent with these transcriptome results. We expect that cis regulation is responsible for unchanged expression in OMA versus maize; and trans regulation is the predominant mechanism behind DEGs. The genome interaction identified here reveals the important consequences of interspecific/intergeneric crosses and potential mechanisms of plant evolution when genomic environments interact.

Monosomic alien addition lines (MAALs) of Oryza rhizomatis in Oryza sativa: production, cytology, alien trait introgression, molecular analysis and breeding application

Key message Development of MAALs and disomic introgression lines derived from the cross between O. sativa and O. rhizomatis to exploit and utilize the valuable traits for rice improvement. The CC genome wild species, Oryza rhizomatis, possesses valuable traits for rice improvement. Unlike other CC genome wild rice, O. rhizomatis is less studied and none of the research has focused on the utilization of this resource in rice breeding. The transfer of novel genes governing the valuable traits from O. rhizomatis is difficult due to high genome incompatibility with O. sativa. Here we report the development of backcross progenies and complete sets of monosomic alien addition lines (MAALs) for the first time from O. rhizomatis in O. sativa line IR31917-45-3-2. Autotetraploid IR31917-45-3-2 (4x = AAAA) was used to generate allotriploid F₁, and the F₁ plant was backcrossed to IR31917-45-3-2 (2x). Forty-seven BC₁F₁ and 73 BC₂F₁ plants were produced with chromosome numbers ranging from 24 to 33 (2x + 9) and 24 to 27 (2x + 3), respectively. A complete set of MAALs were identified by morphological, cytological and marker-based analysis. A total of 116 CC genome-specific InDel markers across the 12 chromosome of rice were used to detect O. rhizomatis chromosome segments in F₁, BC₁F₁, BC₂F₂, MAALs and disomic introgression lines (DILs). Expressions of major phenotypic traits inherited from O. rhizomatis were observed in MAAL-derived DILs. Small chromosomal segments of O. rhizomatis for chromosomes 1, 2, 4, 5, 6, 7, 10 and 12 were detected in DILs, and some of the introgression lines showed insect resistance against brown planthopper and green leafhopper. These newly developed MAALs and DILs will be useful for gene mining and more precise faster transfer of favorable genes to improve rice cultivars.

Ten alien chromosome additions of Gossypium hirsutum-Gossypium bickii developed by integrative uses of GISH and species-specific SSR markers

Gossypium bickii: (2n = 26, G₁G₁), a wild diploid cotton, carries many favourable traits. However, these favourable traits cannot be directly transferred into G. hirsutum (2n = 52, AADD) cultivars due to the differences in genomes. Monosomic alien addition lines (MAALs) are considered an invaluable tool for the introgression of genes of interest from wild relatives into cultivated crops. In this study, the G. hirsutum-G. bickii amphidiploid (2n = 78, AADDG₁G₁) was backcrossed with G. hirsutum to develop alien additions containing individual G. bickii chromosomes in a G. hirsutum background. Genomic in situ hybridization was employed to detect the number of alien chromosomes added to the backcross progenies. A total of 183 G. bickii-specific DNA markers were developed to discriminate the identities of the G. bickii chromosomes added to G. hirsutum and assess the alien chromosome transmissibility. Chromosomes 4G^b and 13G^b showed the highest transmissibility, while chromosomes 1G^b, 7G^b and 11G^b showed the lowest. Ten of the 13 possible G. hirsutum-G. bickii MAALs were isolated and characterized, which will lay the foundation for transferring resistance genes of G. bickii into G. hirsutum, as well as for gene assignment, physical mapping, and selective isolation and mapping of cDNAs for particular G. bickii chromosomes. The strategies of how to use MAALs to develop varieties with the trait of interest from wild species (such as glanded plant-glandless seed) were proposed and discussed.

Genome-Wide Gene Expression Disturbance by Single A1/C1 Chromosome Substitution in Brassica rapa Restituted From Natural B. napus

Alien chromosome substitution (CS) lines are treated as vital germplasms for breeding and genetic mapping. Previously, a whole set of nine Brassica rapa-oleracea monosonic alien addition lines (MAALs, C1-C9) was established in the background of natural B. napus genotype "Oro," after the restituted B. rapa (RBR) for Oro was realized. Herein, a monosomic substitution line with one alien C1 chromosome (Cs1) in the RBR complement was selected in the progenies of MAAL C1 and RBR, by the PCR amplification of specific gene markers and fluorescence in situ hybridization. Cs1 exhibited the whole plant morphology similar to RBR except for the defective stamens without fertile pollen grains, but it produced some seeds and progeny plants carrying the C1 chromosome at high rate besides those without the alien chromosome after pollinated by RBR. The viability of the substitution and its progeny for the RBR diploid further elucidated the functional compensation between the chromosome pairs with high homoeology. To reveal the impact of such aneuploidy on genome-wide gene expression, the transcriptomes of MAAL C1, Cs1 and euploid RBR were analyzed. Compared to RBR, Cs1 had sharply reduced gene expression level across chromosome A1, demonstrating the loss of one copy of A1 chromosome. Both additional chromosome C1 in MAAL and substitutional chromosome C1 in Cs1 caused not only cis-effect but also prevalent trans-effect differentially expressed genes. A dominant gene dosage effects prevailed among low expressed genes across chromosome A1 in Cs1, and moreover, dosage effects for some genes potentially contributed to the phenotype deviations. Our results provided novel insights into the transcriptomic perturbation and gene dosage effects on phenotype in CS related to one naturally evolved allopolyploid.

Inducement and identification of chromosome introgression and translocation of Gossypium australe on Gossypium hirsutum

Background

We previously reported the development of a set of Gossypium hirsutum-G. australe alien chromosome addition lines. Naturally, however, G. hirsutum-G. australe chromosome exchanges were very limited, impeding the stable transference of useful genes from G. australe (G₂G₂ genome) into the most cultivated cotton, G. hirsutum (AADD).

Results

In the present report, the pollen from a pentaploid (2n = AADDG₂) of G. hirsutum-G. australe was irradiated with seven different doses ranging from 10 to 40 Grays and used to pollinate emasculated flowers of G. hirsutum over three consecutive years. Irradiation greatly increased the genetic recombination rates of the G. hirsutum and G. australe chromosomes and a total of 107 chromosome introgression individuals in 192 GISH-negative (with no GISH signal on chromosome) survived individuals, 11 chromosome translocation individuals (containing 12 chromosome translocation events) and 67 chromosome addition individuals were obtained in 70 GISH-positive (with GISH signal(s) on chromosome(s)) survived individuals, which are invaluable for mining desirable genes from G. australe. Multicolor genomic in situ hybridization results showed that there were three types of translocation, whole arm translocation, large alien segment translocation and small alien segment translocation, and that all translocations occurred between the G₂-genome and the A-subgenome chromosomes in G. hirsutum. We also found that higher doses induced much higher rates of chromosome variation but also greatly lowered the seed viability and seedling survivability.

Conclusions

Irradiation has been successfully employed to induce chromosome introgressions and chromosome translocations and promote chromosome exchanges between cultivated and wild species. In addition, by balancing the rates of chromosome introgression and translocation to those of seed set, seed germination, and seedling rates in the M1 generation, we conclude that the dosage of 20 Grays is the most suitable. The established methodology may guide the utilization of the tertiary gene pool of Gossypium species such as G. australe in cotton breeding in the future.

Electronic supplementary material

The online version of this article (10.1186/s12864-017-4398-7) contains supplementary material, which is available to authorized users.

Development of Brassica oleracea-nigra monosomic alien addition lines: genotypic, cytological and morphological analyses

We report the development and characterization of Brassica oleracea - nigra monosomic alien addition lines (MAALs) to dissect the Brassica B genome. Brassica nigra (2n = 16, BB) represents the diploid Brassica B genome which carries many useful genes and traits for breeding but received limited studies. To dissect the B genome from B. nigra, the triploid F₁ hybrid (2n = 26, CCB) obtained previously from the cross B. oleracea var. alboglabra (2n = 18, CC) × B. nigra was used as the maternal parent and backcrossed successively to parental B. oleracea. The progenies in BC₁ to BC₃ generations were analyzed by the methods of FISH and SSR markers to screen the monosomic alien addition lines (MAALs) with each of eight different B-genome chromosomes added to C genome (2n = 19, CC + 1B_1-8), and seven different MAALs were established, except for the one with chromosome B2 which existed in one triple addition. Most of these MAALs were distinguishable morphologically from each other, as they expressed the characters from B. nigra differently and at variable extents. The alien chromosome remained unpaired as a univalent in 86.24% pollen mother cells at diakinesis or metaphase I, and formed a trivalent with two C-genome chromosomes in 13.76% cells. Transmission frequency of all the added chromosomes was far higher through the ovules (averagely 14.40%) than the pollen (2.64%). The B1, B4 and B5 chromosomes were transmitted by female at much higher rates (22.38-30.00%) than the other four (B3, B6, B7, B8) (5.04-8.42%). The MAALs should be valuable for exploiting the genome structure and evolution of B. nigra.

Characterization of eleven monosomic alien addition lines added from Gossypium anomalum to Gossypium hirsutum using improved GISH and SSR markers

BACKGROUND

Gossypium anomalum (BB genome) possesses the desirable characteristics of drought tolerance, resistance to diseases and insect pests, and the potential for high quality fibers. However, it is difficult to transfer the genes associated with these desirable traits into cultivated cotton (G. hirsutum, AADD genome). Monosomic alien addition lines (MAALs) can be used as a bridge to transfer desired genes from wild species into G. hirsutum. In cotton, however, the high number and smaller size of the chromosomes has resulted in difficulties in discriminating chromosomes from wild species in cultivated cotton background, the development of cotton MAALs has lagged far behind many other crops. To date, no set of G. hirsutum-G. anomalum MAALs was reported. Here the amphiploid (AADDBB genome) derived from G. hirsutum × G. anomalum was used to generate a set of G. hirsutum-G. anomalum MAALs through a combination of consecutive backcrossing, genomic in situ hybridization (GISH), morphological survey and microsatellite marker identification.

RESULTS

We improved the GISH technique used in our previous research by using a mixture of two probes from G. anomalum and G. herbaceum (AA genome). The results indicate that a ratio of 4:3 (G. anomalum : G. herbaceum) is the most suitable for discrimination of chromosomes from G. anomalum and the At-subgenome of G. hirsutum. Using this improved GISH technique, 108 MAAL individuals were isolated. Next, 170 G. hirsutum- and G. anomalum-specific codominant markers were obtained and employed for characterization of these MAAL individuals. Finally, eleven out of 13 MAALs were identified. Unfortunately, we were unable to isolate Chrs. 1B^a and 5B^a due to their very low incidences in backcrossing generation, as these remained in a condition of multiple additions.

CONCLUSIONS

The characterized lines can be employed as bridges for the transfer of desired genes from G. anomalum into G. hirsutum, as well as for gene assignment, isolation of chromosome-specific probes, development of chromosome-specific "paints" for fluorochrome-labeled DNA fragments, physical mapping, and selective isolation and mapping of cDNAs/genes for a particular G. anomalum chromosome.

Development of Oryza sativa L. by Oryza punctata Kotschy ex Steud. monosomic addition lines with high value traits by interspecific hybridization

This paper describes the development of monosomic alien addition and disomic introgression lines through a cross between autotetraploid indica rice and Oryza punctata toward tapping valuable traits for rice improvement. Oryza punctata is a distantly related wild Oryza species having BB genome with untapped genetic resources for rice improvement. Low crossability between the cultivated O. sativa and O. punctata restricts the success of transferring many desirable traits into cultivated rice. Artificially induced autotetraploids of an elite breeding line, IR31917-45-3-2, were produced and crossed with O. punctata. Allotriploid F1 plants were backcrossed to IR31917-45-3-2 and generated progenies with extra chromosomes from O. punctata. Twenty BC1F1 and 59 BC2F1 plants were produced with chromosome numbers ranging from 24 (2n) to 29 (2n + 5) and 2n (24) to 26 (2n + 2), respectively. Eleven monosomic alien addition lines (MAALs) were characterized morphologically and cytologically and designated as MAAL 1-12. MAALs were genotyped using O. punctata genome-specific molecular markers and detected chromosome segments inherited from O. punctata. O. punctata introgressions across all the chromosomes of O. sativa were identified except for chromosome 8. The most frequent introgressions were observed in chromosomes 4, 6, 10, and 11, which could be the recombination hotspots between A and B genomes. Some of the qualitative traits such as black hull, purple coleoptile base, purple stigma, long awn, and short grain size from O. punctata were inherited in some disomic introgression lines (DILs). Several DILs inherited genes from O. punctata conferring resistance to brown planthopper, green leafhopper, and diseases such as bacterial blight and blast. This is the first report on successful gene transfer from O. punctata into O. sativa.

Development of Gossypium anomalum-derived microsatellite markers and their use for genome-wide identification of recombination between the G. anomalum and G. hirsutum genomes

We reported the first development of Gossypium anomalum -derived microsatellite markers and identification of recombination between sexually incompatible species by a synthesized hexaploid on genome level. To continue to develop improved cotton varieties, it is essential to transfer desired characters from diploid wild cotton species such as Gossypium anomalum to cultivated allotetraploid cotton species. However, interspecific reproductive barriers limit gene transfer between species. In a previous study, we used colchicine treatment to produce a synthesized hexaploid derived from an interspecific hybrid between Gossypium hirsutum and G. anomalum and demonstrated its hybridity and doubled status using morphological, cytological and molecular marker methods. In the current study, to effectively monitor G. anomalum genome components in the G. hirsutum background, we developed 5974 non-redundant G. anomalum-derived SSR primer pairs using RNA-Seq technology, which were combined with a publicly available physical map. Based on this combined map and segregation data from the BC2F1 population, we identified a set of 230 informative G. anomalum-specific SSR markers distributed on the chromosomes, which cover 95.72% of the cotton genome. After analyzing BC2F1 segregation data, 50 recombination types from 357 recombination events were identified, which cover 81.48% of the corresponding G. anomalum genome. A total of 203 recombination events occurred on chromosome 11, accounting for 56.86% of the recombination events on all chromosomes. Recombination hotspots were observed at marker intervals JAAS1148-NAU5100 on chromosome 1 and JAAS0426-NAU998 on chromosome 2. Therefore, all G. anomalum chromosomes are capable of recombining with At chromosomes in G. hirsutum. This study represents an important step towards introgressing desirable traits into cultivated cotton from the wild cotton species G. anomalum.

A New Synthetic Amphiploid (AADDAA) between Gossypium hirsutum and G. arboreum Lays the Foundation for Transferring Resistances to Verticillium and Drought

Gossypium arboreum, a cultivated cotton species (2n = 26, AA) native to Asia, possesses invaluable characteristics unavailable in the tetraploid cultivated cotton gene pool, such as resistance to pests and diseases and tolerance to abiotic stresses. However, it is quite difficult to transfer favorable traits into Upland cotton through conventional methods due to the cross-incompatibility of G. hirsutum (2n = 52, AADD) and G. arboreum. Here, we improved an embryo rescue technique to overcome the cross-incompatibility between these two parents for transferring favorable genes from G. arboreum into G. hirsutum. Our results indicate that MSB2K supplemented with 0.5 mgl^-1 kinetin and 250 mg^-1 casein hydrolysate is an efficient initial medium for rescuing early (3 d after pollination) hybrid embryos. Eight putative hybrids were successfully obtained, which were further verified and characterized by cytology, molecular markers and morphological analysis. The putative hybrids were subsequently treated with different concentrations of colchicine solution to double their chromosomes. The results demonstrate that four putative hybrid plants were successfully chromosome-doubled by treatment with 0.1% colchicine for 24 h and become amphiploid, which were confirmed by cytological observation, self-fertilization and backcrossing. Preliminary assessments of resistance at seedling stage indicate that the synthetic amphiploid showed highly resistant to Verticillium and drought. The synthetic amphiploid between G. hirsutum × G. arboreum would lay the foundation for developing G. arboreum-introgressed lines with the uniform genetic background of G. hirsutum acc TM-1, which would greatly enhance and simplify the mining, isolation, characterization, cloning and use of G. arboreum-specific desirable genes in future cotton breeding programs.

A new synthetic allotetraploid (A1A1G2G2) between Gossypium herbaceum and G. australe: bridging for simultaneously transferring favorable genes from these two diploid species into upland cotton

Gossypium herbaceum, a cultivated diploid cotton species (2n = 2x = 26, A₁A₁), has favorable traits such as excellent drought tolerance and resistance to sucking insects and leaf curl virus. G. australe, a wild diploid cotton species (2n = 2x = 26, G₂G₂), possesses numerous economically valuable characteristics such as delayed pigment gland morphogenesis (which is conducive to the production of seeds with very low levels of gossypol as a potential food source for humans and animals) and resistance to insects, wilt diseases and abiotic stress. Creating synthetic allotetraploid cotton from these two species would lay the foundation for simultaneously transferring favorable genes into cultivated tetraploid cotton. Here, we crossed G. herbaceum (as the maternal parent) with G. australe to produce an F₁ interspecific hybrid and doubled its chromosome complement with colchicine, successfully generating a synthetic tetraploid. The obtained tetraploid was confirmed by morphology, cytology and molecular markers and then self-pollinated. The S₁ seedlings derived from this tetraploid gradually became flavescent after emergence of the fifth true leaf, but they were rescued by grafting and produced S₂ seeds. The rescued S₁ plants were partially fertile due to the existence of univalents at Metaphase I of meiosis, leading to the formation of unbalanced, nonviable gametes lacking complete sets of chromosomes. The S₂ plants grew well and no flavescence was observed, implying that interspecific incompatibility, to some extent, had been alleviated in the S₂ generation. The synthetic allotetraploid will be quite useful for polyploidy evolutionary studies and as a bridge for transferring favorable genes from these two diploid species into Upland cotton through hybridization.

Evaluation of cotton leaf curl virus resistance in BC1, BC2, and BC3 progenies from an interspecific cross between Gossypium arboreum and Gossypium hirsutum

Cotton leaf curl virus disease (CLCuD) is an important constraint to cotton production. The resistance of G. arboreum to this devastating disease is well documented. In the present investigation, we explored the possibility of transferring genes for resistance to CLCuD from G. arboreum (2n = 26) cv 15-Mollisoni into G. hirsutum (2n = 52) cv CRSM-38 through conventional breeding. We investigated the cytology of the BC₁ to BC₃ progenies of direct and reciprocal crosses of G. arboreum and G. hirsutum and evaluated their resistance to CLCuD. The F₁ progenies were completely resistant to this disease, while a decrease in resistance was observed in all backcross generations. As backcrossing progressed, the disease incidence increased in BC₁ (1.7–2.0%), BC₂ (1.8–4.0%), and BC₃ (4.2–7.0%). However, the disease incidence was much lower than that of the check variety CIM-496, with a CLCuD incidence of 96%. Additionally, the disease incidence percentage was lower in the direct cross 2(G. arboreum)×G. hirsutum than in that of G. hirsutum×G. arboreum. Phenotypic resemblance of BC₁ ∼BC₃ progenies to G. arboreum confirmed the success of cross between the two species. Cytological studies of CLCuD-resistant plants revealed that the frequency of univalents and multivalents was high in BC₁, with sterile or partially fertile plants, but low in BC₂ (in both combinations), with shy bearing plants. In BC₃, most of the plants exhibited normal bearing ability due to the high frequency of chromosome associations (bivalents). The assessment of CLCuD through grafting showed that the BC₁ to BC₃ progenies were highly resistant to this disease. Thus, this study successfully demonstrates the possibility of introgressing CLCuD resistance genes from G. arboreum to G. hirsutum.