The development of 7E chromosome-specific molecular markers for Thinopyrum elongatum based on SLAF-seq technology

Cytogenetic and Genomic Characterization of a Novel Wheat-Tetraploid Thinopyrum elongatum 1BS⋅1EL Translocation Line with Stripe Rust Resistance

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is a destructive wheat disease pathogen. Thinopyrum elongatum is a valuable germplasm including diploid, tetraploid, and decaploid with plenty of biotic and abiotic resistance. In a previous study, we generated a stripe rust-resistant wheat-tetraploid Th. elongatum 1E/1D substitution line, K17-841-1. To further apply the wild germplasm for wheat breeding, we selected and obtained a new homozygous wheat-tetraploid Th. elongatum translocation line, T1BS⋅1EL, using genomic in situ hybridization, fluorescence in situ hybridization (FISH), oligo-FISH painting, and the wheat 55K single nucleotide polymorphism genotyping array. The T1BS⋅1EL is highly resistant to stripe rust at the seedling and adult stages. Pedigree and molecular marker analyses revealed that the resistance gene was located on the chromosome arm 1EL of tetraploid Th. elongatum, tentatively named Yr1EL. In addition, we developed and validated 32 simple sequence repeat markers and two kompetitive allele-specific PCR assays that were specific to the tetraploid Th. elongatum chromosome arm 1EL to facilitate marker-assisted selection for alien 1EL stripe rust resistance breeding. This will help us explore and locate the stripe rust resistance gene mapping on the 1E chromosome and deploy it in the wheat breeding program.

Construction of a high-density genetic map based on large-scale marker development in Coix lacryma-jobi L. using specific-locus amplified fragment sequencing (slaf-seq)

Coix lacryma-jobi L. is one of the most economically and medicinally important corns. This study constructed a high-density genetic linkage map of C. lacryma-jobi based on a cross between the parents 'Qianyi No. 2' × 'Wenyi No. 2' and their F2 progeny through high-throughput sequencing and the construction of a specific-locus amplified fragment (SLAF) library. After pre-processing, 325.49 GB of raw data containing 1628 M reads were obtained. A total of 22,944 high-quality SLAFs were identified, among which 3952 SLAFs and 3646 polymorphic markers met the requirements for the construction of a genetic linkage map. The integrated map contained 3605 high-quality SLAFs, which were grouped into ten genetic linkage groups. The total length of the map was 1620.39 cM, with an average distance of 0.45 cM and an average of 360.5 markers per linkage group. This report presents the first high-density genetic map of C. lacryma-jobi. This map was constructed using an F2 population and SLAF-seq approach, which allows the development of a large number of polymorphic markers in a short period. These results provide a platform for precise gene/quantitative trait locus (QTL) mapping, map-based gene separation, and molecular breeding in C. lacryma-jobi. They also help identify a target gene for tracking, splitting quantitative traits, and estimating the phenotypic effects of each QTL for QTL mapping. They are of great significance for improving the efficiency of discovering and utilizing excellent gene resources of C. lacryma-jobi.

Identification and introgression of a novel leaf rust resistance gene from Thinopyrum intermedium chromosome 7Js into wheat

KEY MESSAGE

A novel leaf rust resistance locus located on a terminal segment (0-69.29 Mb) of Thinopyrum intermedium chromosome arm 7JsS has been introduced into wheat genome for disease resistance breeding. Xiaoyan 78829, a wheat-Thinopyrum intermedium partial amphiploid, exhibits excellent resistance to fungal diseases in wheat. To transfer its disease resistance to common wheat (Triticum aestivum), we previously developed a translocation line WTT26 using chromosome engineering. Disease evaluation showed that WTT26 was nearly immune to 14 common races of leaf rust pathogen (Puccinia triticina) and highly resistant to Ug99 race PTKST of stem rust pathogen (P. graminis f. sp. tritici) at the seedling stage. It also displayed high adult plant resistance to powdery mildew (caused by Blumeria graminis f. sp. tritici). Cytogenetic and molecular marker analysis revealed that WTT26 carried a T4BS·7JsS chromosome translocation. Once transferred into the susceptible wheat genetic background, chromosome 7JsS exhibited its resistance to leaf rust, indicating that the resistance locus was located on this alien chromosome. To enhance the usefulness of this locus in wheat breeding, we further developed several new translocation lines with small Th. intermedium segments using irradiation and developed 124 specific markers using specific-locus amplified fragment sequencing, which increased the marker density of chromosome 7JsS. Furthermore, a refined physical map of chromosome 7JsS was constructed with 74 specific markers, and six bins were thus arranged according to the co-occurrence of markers and alien chromosome segments. Combining data from specific marker amplification and resistance evaluation, we mapped a new leaf rust resistance locus in the 0-69.29 Mb region on chromosome 7JsS. The translocation lines carrying the new leaf rust resistance locus and its linked markers will contribute to wheat disease-resistance breeding.

Development and Characterization of a Novel Wheat-Tetraploid Thinopyrum elongatum 6E (6D) Disomic Substitution Line with Stripe Rust Resistance at the Adult Stage

Stripe rust, which is caused by Puccinia striiformis f. sp. tritici, is one of the most devastating foliar diseases of common wheat worldwide. Breeding new wheat varieties with durable resistance is the most effective way of controlling the disease. Tetraploid Thinopyrum elongatum (2n = 4x = 28, EEEE) carries a variety of genes conferring resistance to multiple diseases, including stripe rust, Fusarium head blight, and powdery mildew, which makes it a valuable tertiary genetic resource for enhancing wheat cultivar improvement. Here, a novel wheat-tetraploid Th. elongatum 6E (6D) disomic substitution line (K17-1065-4) was characterized using genomic in situ hybridization and fluorescence in situ hybridization chromosome painting analyses. The evaluation of disease responses revealed that K17-1065-4 is highly resistant to stripe rust at the adult stage. By analyzing the whole-genome sequence of diploid Th. elongatum, we detected 3382 specific SSR sequences on chromosome 6E. Sixty SSR markers were developed, and thirty-three of them can accurately trace chromosome 6E of tetraploid Th. elongatum, which were linked to the disease resistance gene(s) in the wheat genetic background. The molecular marker analysis indicated that 10 markers may be used to distinguish Th. elongatum from other wheat-related species. Thus, K17-1065-4 carrying the stripe rust resistance gene(s) is a novel germplasm useful for breeding disease-resistant wheat cultivars. The molecular markers developed in this study may facilitate the mapping of the stripe rust resistance gene on chromosome 6E of tetraploid Th. elongatum.

Systemic development of wheat-Thinopyrum elongatum translocation lines and their deployment in wheat breeding for Fusarium head blight resistance

Fusarium head blight (FHB), mainly caused by Fusarium graminearum, is one of the most destructive diseases of wheat (Triticum aestivum) around the world. FHB causes significant yield losses and reduces grain quality. The lack of resistance resources is a major bottleneck for wheat FHB resistance breeding. As a wheat relative, Thinopyrum elongatum contains many genes that can be used for wheat improvement. Although the novel gene Fhb-7EL was mapped on chromosome 7EL of Th. elongatum, successful transfer of the FHB resistance gene into commercial wheat varieties has not been reported. In this study, we developed 836 wheat-Th. elongatum translocation lines of various types by irradiating the pollen of the wheat-Th. elongatum addition line CS-7EL at the flowering stage, among which 81 were identified as resistant to FHB. By backcrossing the FHB-resistant lines with the main cultivar Jimai 22, three wheat-Th. elongatum translocation lines, Zhongke 1878, Zhongke 166, and Zhongke 545, were successfully applied in wheat breeding without yield penalty. Combining karyotype and phenotype analyses, we mapped the Fhb-7EL gene to the distal end of chromosome 7EL. Five molecular markers linked with the FHB resistance interval were developed, which facilitates molecular marker-assisted breeding. Altogether, we successfully applied alien chromatin with FHB resistance from Th. elongatum in wheat breeding without yield penalty. These newly developed FHB-resistant wheat-Th. elongatum translocation lines, Zhongke 1878, Zhongke 166, and Zhongke 545, can be used as novel resistance resources for wheat breeding.

Cytogenetic Characterization and Molecular Marker Development for a Wheat-T. boeoticum 4Ab (4B) Disomic Substitution Line with Stripe Rust Resistance

Triticum boeoticum (2n = 2x = 14, A^bA^b) is an important relative of wheat. This species tolerates many different types of environmental stresses, including drought, salt, and pathogenic infection, and is lower in dietary fiber and higher in antioxidants, protein (15 to 18%), lipids, and trace elements than common wheat. However, the gene transfer rate from this species to common wheat is low, and few species-specific molecular markers are available. In this study, the wheat-T. boeoticum substitution line Z1889, derived from a cross between the common wheat cultivar Crocus and T. boeoticum line G52, was identified using multicolor fluorescence in situ hybridization, multicolor genomic in situ hybridization, and a 55K single-nucleotide polymorphism array. Z1889 was revealed to be a 4A^b (4B) substitution line with a high degree of resistance to stripe rust pathogen strains prevalent in China. In addition, 22 4A^b chromosome-specific molecular markers and 11 T. boeoticum genome-specific molecular markers were developed from 1,145 4A^b chromosome-specific fragments by comparing the sequences generated by specific-length amplified fragment sequencing, with an efficiency of up to 55.0%. Furthermore, the specificity of these markers was verified in four species containing the A^b genome. These markers not only can be used for the detection of the 4A^b chromosome but also provide a basis for molecular marker-assisted, selection-based breeding in wheat.

Genetic analysis of resistance to powdery mildew on 7Mg chromosome of wheat-Aegilops geniculata, development and utilization of specific molecular markers

BACKGROUND

Powdery mildew caused by Blumeria graminis f. sp. tritici (Bgt) is prevalent in the main wheat-producing regions of China, resulting in severe yield losses in recent years. Mining and utilization of resistant genes from wild relatives of wheat is the most environmentally sound measure to control disease. Aegilops geniculata Roth (2n = 2x = 28, U^gU^gM^gM^g) is an essential and valuable disease-resistance gene donor for wheat improvement as a close relative species.

RESULTS

In this study, to validate powdery mildew resistance locus on chromosome 7M^g, two genetic populations were constructed and through crossing wheat - Ae. geniculata 7M^g disomic addition line NA0973-5-4-1-2-9-1 and 7M^g (7 A) alien disomic substitution line W16998 with susceptible Yuanfeng175 (YF175, authorized varieties from Shaanxi province in 2005), respectively. Cytological examination, in situ hybridization (ISH), and functional molecular markers analysis revealed that the plants carrying chromosome 7M^g showed high resistance to powdery mildew in both F₁ and F₂ generation at the seedling stage. Besides, 84 specific markers were developed to identify the plants carrying chromosome 7M^g resistance based on the specific-locus amplified fragment sequencing (SLAF-seq) technique. Among them, four markers were selected randomly to check the reliability in F₂ segregating populations derived from YF175/NA0973-5-4-1-2-9-1 and YF175/W16998. In summary, the above analysis confirmed that a dominant high powdery mildew resistance gene was located on chromosome 7M^g of Ae. geniculata.

CONCLUSION

The results provide a basis for mapping the powdery mildew resistance gene mapping on chromosome 7M^g and specific markers for their utilization in the future.

Phylogenetic relationship and taxonomic status of Gymnocypris eckloni (Schizothoracinae) based on specific locus amplified fragments sequencing

Accurately delimiting phylogenetic relationships and taxonomic status is important for understanding species diversity and distributions and devising effective strategies for biodiversity conservation. However, species delimitation is controversial in Gymnocypris eckloni, a schizothoracine fish endemic to the Qinghai–Tibetan Plateau. The aim of this study is robustly identifying the phylogeny of G. eckloni in the Yellow River (YR) population and Qaidam basin (QB) population. The specific-locus amplified fragments sequencing (SLAF-seq) is employed with comprehensively sampling of schizothoracine fishes. In total, 350,181,802 clean reads and 5,114,096 SNPs are identified from SLAF-seq. Phylogenetic analysis recovers a non-monophyletic population of G. eckloni between YR and QB populations, representing an independent phylogenetic relationship between the two populations. Species delimitation analyses by SNAPPER and GMYC methods using the genome-wide SNP data confirm that their taxonomic statuses are separated. This study highlights the importance of further reconsidering clearer taxonomy, which would improve the genetic diversity conservation of Tibetan highland fishes.

Cytogenetic identification and molecular marker development of a novel wheat-Leymus mollis 4Ns(4D) alien disomic substitution line with resistance to stripe rust and Fusarium head blight

Leymus mollis (Trin.) Pilg. (2n = 4x = 28, NsNsXmXm) potentially harbours useful genes that might contribute to the improvement of wheat. We describe M862 as a novel wheat-L. mollis alien disomic substitution line from a cross between wheat cv. 7182 and octoploid Tritileymus M47. Cytological observations indicate that M862 has a chromosome constitution of 2n = 42 = 21II. Two 4D chromosomes of wheat substituted by two L. mollis Ns chromosomes were observed, using the GISH and ND-FISH analyses. Molecular marker, 55K SNP array and wheat-P. huashanica liquid array (GenoBaits^®WheatplusPh) analyses further indicate that the alien chromosomes are L. mollis 4Ns. Therefore, it was deduced that M862 was a wheat-L. mollis 4Ns(4D) alien disomic substitution line. There were also changes in chromosomes 1A, 1D, 2B and 5A detected by ND-FISH analysis. Transcriptome sequencing showed that the structural variation of 1D, 1A and 5A may have smaller impact on gene expression than that for 2B. In addition, a total of 16 markers derived from Lm#4Ns were developed from transcriptome sequences, and these proved to be highly effective for tracking the introduced chromosome. M862 showed reduced height, larger grains (weight and width), and was highly resistance to CYR32 and CYR34 stripe rust races at the seedling stage and mixed stripe rust races (CYR32, CYR33 and CYR34) at the adult stage. It was also resistance to Fusarium head blight (FHB). This alien disomic substitution line M862 may be exploited as an important genetic material in the domestication of stipe rust and FHB resistance wheat varieties.

Construction of High-Density Genetic Map and Identification of a Bruchid Resistance Locus in Mung Bean (Vigna radiata L.)

Mung bean (Vigna radiata L.) is an economically important grain legume cultivated in Asian countries. High-density genetic linkage is a valuable and effective tool for mapping quantitative trait loci (QTL). In the current study, a high-resolution genetic map containing 4,180 single-nucleotide polymorphisms (SNPs) was assigned to 11 linkage groups (LGs) and spanning 1,751.39 cM in length was constructed for mung bean, and the average distance between adjacent markers was 0.42 cM. Bruchids (Callosobruchus spp.) cause significant damage to and loss of legume seeds. A locus for bruchid resistance was detected. The gene Vradi05g03810, encoding a probable resistance-specific protein, was found to be the most likely key candidate gene in mung beans. A 69-bp sequence deletion was identified in the coding region by comparing the cDNA sequences of bruchid-resistant and bruchid-susceptible lines. This SNP-based high-density linkage map is one of the first to be constructed across the mung bean genome. This map will not only facilitate the genetic mapping of genes or complex loci that control important agronomic traits but also offer a tool for promoting future genetics and comparative genomic studies in Vigna.

Identification and DNA Marker Development for a Wheat-Leymus mollis 2Ns (2D) Disomic Chromosome Substitution

Leymus mollis (2n = 4x = 28, NsNsXmXm), a wild relative of common wheat (Triticum aestivum L.), carries numerous loci which could potentially be used in wheat improvement. In this study, line 17DM48 was isolated from the progeny of a wheat and L. mollis hybrid. This line has 42 chromosomes forming 21 bivalents at meiotic metaphase I. Genomic in situ hybridization (GISH) demonstrated the presence of a pair chromosomes from the Ns genome of L. mollis. This pair substituted for wheat chromosome 2D, as shown by fluorescence in situ hybridization (FISH), DNA marker analysis, and hybridization to wheat 55K SNP array. Therefore, 17DM48 is a wheat-L. mollis 2Ns (2D) disomic substitution line. It shows longer spike and a high level of stripe rust resistance. Using specific-locus amplified fragment sequencing (SLAF-seq), 13 DNA markers were developed to identify and trace chromosome 2Ns of L. mollis in wheat background. This line provides a potential bridge germplasm for genetic improvement of wheat stripe rust resistance.

Candidate powdery mildew resistance gene in wheat landrace cultivar Hongyoumai discovered using SLAF and BSR-seq

BACKGROUND

Wheat powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is an important disease affecting wheat production. Planting resistant cultivars is an effective, safe, and economical method to control the disease. Map construction using next-generation sequencing facilitates gene cloning based on genetic maps and high-throughput gene expression studies. In this study, specific-locus amplified fragment sequencing (SLAF) was used to analyze Huixianhong (female parent), Hongyoumai (male parent) and two bulks (50 homozygous resistant and 50 susceptible F_2:3 segregating population derived from Huixianhong × Hongyoumai to determine a candidate gene region for resistance to powdery mildew on the long arm of chromosome 7B in wheat landrace Hongyoumai. Gene expressions of candidate regions were obtained using bulked segregant RNA-seq in 10 homozygous resistant and 10 susceptible progeny inoculated by Bgt.. Candidate genes were obtained using homology-based cloning in two parents.

RESULTS

A 12.95 Mb long candidate region in chromosome 7BL was identified, and five blocks in SLAF matched the scaffold of the existing co-segregation marker Xmp1207. In the candidate region, 39 differentially expressed genes were identified using RNA-seq, including RGA4 (Wheat_Chr_Trans_newGene_16173)-a disease resistance protein whose expression was upregulated in the resistant pool at 16 h post inoculation with Bgt. Quantitative reverse transcription (qRT)-PCR was used to further verify the expression patterns in Wheat_Chr_Trans_newGene_16173 that were significantly different in the two parents Hongyoumai and Huixianhong. Two RGA4 genes were cloned based on the sequence of Wheat_Chr_Trans_newGene_16173, respectively from two parent and there was one amino acid mutation: S to G in Huixianhong on 510 loci.

CONCLUSION

The combination of SLAF and BSR-seq methods identified a candidate region of pmHYM in the chromosome 7BL of wheat landrace cultivar Hongyoumai. Comparative analysis between the scaffold of co-segregating marker Xmp1207 and SLAF-seq showed five matching blocks. qRT-PCR showed that only the resistant gene Wheat_Chr_Trans_newGene_16173 was significantly upregulated in the resistant parent Hongyoumai after inoculation with Bgt, and gene cloning revealed a difference in one amino acid between the two parent genes, indicating it was involved in the resistance response and may be the candidate resistance gene pmHYM.

Investigation of genetic relationships within three Miscanthus species using SNP markers identified with SLAF-seq

BACKGROUND

Miscanthus, which is a leading dedicated-energy grass in Europe and in parts of Asia, is expected to play a key role in the development of the future bioeconomy. However, due to its complex genetic background, it is difficult to investigate phylogenetic relationships in this genus. Here, we investigated 50 Miscanthus germplasms: 1 female parent (M. lutarioriparius), 30 candidate male parents (M. lutarioriparius, M. sinensis, and M. sacchariflorus), and 19 offspring. We used high-throughput Specific-Locus Amplified Fragment sequencing (SLAF-seq) to identify informative single nucleotide polymorphisms (SNPs) in all germplasms.

RESULTS

We identified 257,889 SLAF tags, of which 87,162 were polymorphic. Each tag was 264-364 bp long. The obtained 724,773 population SNPs were used to investigate genetic relationships within three species of Miscanthus. We constructed a phylogenetic tree of the 50 germplasms using the obtained SNPs and grouped them into two clades: one clade comprised of M. sinensis alone and the other one included the offspring, M. lutarioriparius, and M. sacchariflorus. Genetic cluster analysis had revealed that M. lutarioriparius germplasm C3 was the most likely male parent of the offspring.

CONCLUSIONS

As a high-throughput sequencing method, SLAF-seq can be used to identify informative SNPs in Miscanthus germplasms and to rapidly characterize genetic relationships within this genus. Our results will support the development of breeding programs with the focus on utilizing Miscanthus cultivars with elite biomass- or fiber-production potential for the developing bioeconomy.

Identification of a Wheat-Psathyrostachys huashanica 7Ns Ditelosomic Addition Line Conferring Early Maturation by Cytological Analysis and Newly Developed Molecular and FISH Markers

Early maturation is an important objective in wheat breeding programs that could facilitate multiple-cropping systems, decrease disaster- and disease-related losses, ensure stable wheat production, and increase economic benefits. Exploitation of novel germplasm from wild relatives of wheat is an effective means of breeding for early maturity. Psathyrostachys huashanica Keng f. ex P. C. KUO (2n=2x=14, NsNs) is a promising source of useful genes for wheat genetic improvement. In this study, we characterized a novel wheat-P. huashanica line, DT23, derived from distant hybridization between common wheat and P. huashanica. Fluorescence in situ hybridization (FISH) and sequential genomic in situ hybridization (GISH) analyses indicated that DT23 is a stable wheat-P. huashanica ditelosomic addition line. FISH painting and PCR-based landmark unique gene markers analyses further revealed that DT23 is a wheat-P. huashanica 7Ns ditelosomic addition line. Observation of spike differentiation and the growth period revealed that DT23 exhibited earlier maturation than the wheat parents. This is the first report of new earliness per se (Eps) gene(s) probably associated with a group 7 chromosome of P. huashanica. Based on specific locus-amplified fragment sequencing technology, 45 new specific molecular markers and 19 specific FISH probes were developed for the P. huashanica 7Ns chromosome. Marker validation analyses revealed that two specific markers distinguished the Ns genome chromosomes of P. huashanica and the chromosomes of other wheat-related species. These newly developed FISH probes specifically detected Ns genome chromosomes of P. huashanica in the wheat background. The DT23 line will be useful for breeding early maturing wheat. The specific markers and FISH probes developed in this study can be used to detect and trace P. huashanica chromosomes and chromosomal segments carrying elite genes in diverse materials.

Molecular cytogenetics for a wheat-Aegilops geniculata 3Mg alien addition line with resistance to stripe rust and powdery mildew

BACKGROUND

Aegilops geniculata Roth is closely related to common wheat (Triticum aestivum L.) and is a valuable genetic resource for improvement of wheat.

RESULTS

In this study, the W19513 line was derived from the BC₁F₁₀ progeny of a cross between wheat 'Chinese Spring' and Ae. geniculata SY159. Cytological examination showed that W19513 contained 44 chromosomes. Twenty-two bivalents were formed at the first meiotic metaphase I in the pollen mother cellsand the chromosomes were evenly distributed to opposite poles at meiotic anaphase I. Genomic in situ hybridization demonstrated that W19513 carried a pair of alien chromosomes from the M genome. Fluorescence in situ hybridization confirmed detection of variation in chromosomes 4A and 6B. Functional molecular marker analysis using expressed sequence tag-sequence-tagged site and PCR-based landmark unique gene primers revealed that the alien gene belonged to the third homologous group. The marker analysis confirmed that the alien chromosome pair was 3M^g. In addition, to further explore the molecular marker specificity of chromosome 3M^g, based on the specific locus amplified fragment sequencing technique, molecular markers specific for W19513 were developed with efficiencies of up to 47.66%. The W19513 line was inoculated with the physiological race E09 of powdery mildew (Blumeria graminis f. sp. tritici) at the seedling stage and showed moderate resistance. Field inoculation with a mixture of the races CYR31, CYR32, CYR33, and CYR34 of the stripe rust fungus (Puccinia striiformis f. sp. triticii) revealed that the line W19513 showed strong resistance.

CONCLUSIONS

This study provides a foundation for use of the line W19513 in future genetic research and wheat improvement.

SNP detection and population structure evaluation of Salix gordejevii Y. L. Chang et Skv. in Hunshandake Sandland, Inner Mongolia, China

Single nucleotide polymorphisms (SNPs) are the most abundant and richest form of genomic polymorphism and, hence, are highly favorable markers for genetic map construction and genome-wide association studies. Based on the DNA specific-locus amplified fragment sequencing (SLAF-seq) for large-scale SNP detection, the genetic diversity and population structure of Salix gordejevii Y. L. Chang et Skv., a valuable sand-fixing shrub, was assessed in 199 accessions from 20 populations in Hunshandake Sandland of northern China. A total of 623.15 M reads resulted in 30.49 × sequencing depth on average and a mean Q30 of 95.70%, and 2,287,715 SNPs in 178,509 polymorphic SLAF tags were obtained. By discarding minor allele frequency > 0.05 and integrity > 0.8, a total of 93,600 SNPs were retained for population genetic analyses, which revealed that 199 individuals could be divided into six groups based on cross-validation errors. However, this grouping pattern did not match the geographical distribution, indicating that there is no apparent geographic barrier in the blank areas where S. gordejevii was not distributed in Hunshandake Sandland. In addition, the physical distance of linkage disequilibrium decay in the analyzed S. gordejevii individuals was 18.5 kb when r ² = 0.1. The linkage disequilibrium decay distances for different chromosomes varied from 4.6 kb (chromosome 16) to 37.8 kb (chromosome 3). The obtained SNPs offer suitable marker resources for further genetic and genomic studies and will benefit S. gordejevii breeding programs.

Chromosomal composition analysis and molecular marker development for the novel Ug99-resistant wheat-Thinopyrum ponticum translocation line WTT34

A novel Ug99-resistant wheat-Thinopyrum ponticum translocation line was produced, its chromosomal composition was analyzed and specific markers were developed. Stem rust caused by Puccinia graminis f. sp. tritici Eriks. & E. Henn (Pgt) has seriously threatened global wheat production since Ug99 race TTKSK was first detected in Uganda in 1998. Thinopyrum ponticum is near immune to Ug99 races and may be useful for enhancing wheat disease resistance. Therefore, developing new wheat-Th. ponticum translocation lines that are resistant to Ug99 is crucial. In this study, a novel wheat-Th. ponticum translocation line, WTT34, was produced. Seedling and field evaluation revealed that WTT34 is resistant to Ug99 race PTKST. The resistance was derived from the alien parent Th. ponticum. Screening WTT34 with markers linked to Sr24, Sr25, Sr26, Sr43, and SrB resulted in the amplification of different DNA fragments from Th. ponticum, implying WTT34 carries at least one novel stem rust resistance gene. Genomic in situ hybridization (GISH), multicolor fluorescence in situ hybridization (mc-FISH), and multi-color GISH (mc-GISH) analyses indicated that WTT34 carries a T5DS·5DL-Th translocation, which was consistent with wheat660K single-nucleotide polymorphism (SNP) array results. The SNP array also uncovered a deletion event in the terminal region of chromosome 1D. Additionally, the homeology between alien segments and the wheat chromosomes 2A and 5D was confirmed. Furthermore, 51 PCR-based markers derived from the alien segments of WTT34 were developed based on specific-locus amplified fragment sequencing (SLAF-seq). These markers may enable wheat breeders to rapidly trace Th. ponticum chromosomal segments carrying Ug99 resistance gene(s).

Introgression of Thinopyrum elongatum DNA fragments carrying resistance to fusarium head blight into Triticum aestivum cultivar Chinese Spring is associated with alteration of gene expression

The tall wheatgrass species Thinopyrum elongatum carries on the long arm of chromosome 7E, a locus that contributes strongly to resistance to fusarium head blight (FHB), a devastating fungal disease affecting wheat crops in all temperate areas of the world. Introgression of Th. elongatum 7E chromatin into chromosome 7D of wheat was induced by the ph1b mutant of CS. Recombinants between chromosome 7E and wheat chromosome 7D, induced by the ph1b mutation, were monitored by a combination of molecular markers and phenotyping for FHB resistance. Progeny of up to five subsequent generations derived from two lineages, 64-8 and 32-5, were phenotyped for FHB symptoms and genotyped using published and novel 7D- and 7E-specific markers. Fragments from the distal end of 7EL, still carrying FHB resistance and estimated to be less than 114 and 66 Mbp, were identified as introgressed into wheat chromosome arm 7DL of progeny derived from 64-8 and 32-5, respectively. Gene expression analysis revealed variation in the expression levels of genes from the distal ends of 7EL and 7DL in the introgressed progeny. The 7EL introgressed material will facilitate the use of the 7EL FHB resistance locus in wheat breeding programs.

Transfer of fusarium head blight resistance from Thinopyrum elongatum to bread wheat cultivar Chinese Spring

The diploid form of tall wheatgrass, Thinopyrum elongatum (Host) D.R. Dewey (2n = 2x = 14, EE genome), has a high level of resistance to fusarium head blight. The symptoms did not spread beyond the inoculated florets following point inoculation. Using a series of E-genome chromosome additions in a bread wheat cultivar Chinese Spring (CS) background, the resistance was found to be localized to the long arm of chromosome 7E. The CS mutant ph1b was used to induce recombination between chromosome 7E, present in the 7E(7D) substitution and homoeologous wheat chromosomes. Multivalent chromosome associations were detected in the BC₁ hybrids, confirming the effectiveness of the ph1b mutant. Genetic markers specific for chromosome 7E were used to estimate the size of the 7E introgression in the wheat genome. Using single sequence repeat (SSR) markers specific for homoeologous wheat chromosome 7, introgressions were detected on wheat chromosomes 7A, 7B, and 7D. Some of the introgression lines were resistant to fusarium head blight.

Exploiting the genome of Thinopyrum elongatum to expand the gene pool of hexaploid wheat

One hundred and thirty four introgressions from Thinopyrum elongatum have been transferred into a wheat background and were characterised using 263 SNP markers. Species within the genus Thinopyrum have been shown to carry genetic variation for a very wide range of traits including biotic and abiotic stresses and quality. Research has shown that one of the species within this genus, Th. elongatum, has a close relationship with the genomes of wheat making it a highly suitable candidate to expand the gene pool of wheat. Homoeologous recombination, in the absence of the Ph1 gene, has been exploited to transfer an estimated 134 introgressions from Th. elongatum into a hexaploid wheat background. The introgressions were detected and characterised using 263 single nucleotide polymorphism markers from a 35 K Axiom^® Wheat-Relative Genotyping Array, spread across seven linkage groups and validated using genomic in situ hybridisation. The genetic map had a total length of 187.8 cM and the average chromosome length was 26.8 cM. Comparative analyses of the genetic map of Th. elongatum and the physical map of hexaploid wheat confirmed previous work that indicated good synteny at the macro-level, although Th. elongatum does not contain the 4A/5A/7B translocation found in wheat.

Molecular Cytogenetic Identification of Wheat-Aegilops Biuncialis 5Mb Disomic Addition Line with Tenacious and Black Glumes

Production of wheat-alien disomic addition lines is of great value to the exploitation and utilization of elite genes originated from related species to wheat. In this study, a novel wheat-Aegilops biuncialis 5Mb disomic addition line WA317 was characterized by in situ hybridization (ISH) and specific-locus amplified fragment sequencing (SLAF-seq) markers. Compared to its parent Chinese Spring (CS), the glumes of WA317 had black color and were difficult to remove after harvesting, suggesting chromosome 5Mb carried gene(s) related to glume development and Triticeae domestication process. A total of 242 Ae. biuncialis SLAF-based markers (298 amplified patterns) were developed and further divided into four categories by Ae. biuncialis Y17, Ae. umbellulata Y139 and Ae. comosa Y258, including 172 markers amplifying the same bands of U and M genome, six and 102 markers amplifying U-specific and M-specific bands, respectively and eighteen markers amplifying specific bands in Y17. Among them, 45 markers had the specific amplifications in WA317 and were 5Mb specific markers. Taken together, line WA317 with tenacious and black glumes should serve as the foundation for understanding of the Triticeae domestication process and further exploitation of primitive alleles for wheat improvement. Ae. biuncialis SLAF-based markers can be used for studying syntenic relationships between U and M genomes as well as rapid tracking of U and M chromosomal segments in wheat background.

Cytogenetic Analysis and Molecular Marker Development for a New Wheat-Thinopyrum ponticum 1Js (1D) Disomic Substitution Line With Resistance to Stripe Rust and Powdery Mildew

Thinopyrum ponticum (2n = 10x = 70), a member of the tertiary gene pool of wheat (Triticum aestivum L.), harbors many biotic and abiotic stress resistance genes. CH10A5, a novel disomic substitution line from a cross of T. aestivum cv. 7182 and Th. ponticum, was characterized by cytogenetic identification, in situ hybridization, molecular marker analysis, and morphological investigation of agronomic traits and disease resistance. Cytological observations showed that CH10A5 contained 42 chromosomes and formed 21 bivalents at meiotic metaphase I. Genome in situ hybridization (GISH) analysis indicated that two of its chromosomes came from the J^s genome of Th. ponticum, and wheat 15K array mapping and fluorescence in situ hybridization (FISH) revealed that chromosome 1D was absent from CH10A5. Polymorphic analysis of molecular markers indicated that the pair of alien chromosomes belonged to homoeologous group one, designated as 1J^s. Thus, CH10A5 was a wheat-Th. ponticum 1J^s (1D) disomic substitution line. Field disease resistance trials demonstrated that the introduced Th. ponticum chromosome 1J^s was probably responsible for resistance to both stripe rust and powdery mildew at the adult stage. Based on specific-locus amplified fragment sequencing (SLAF-seq), 507 STS molecular markers were developed to distinguish chromosome 1J^s genetic material from that of wheat. Of these, 49 STS markers could be used to specifically identify the genetic material of Th. ponticum. CH10A5 will increase the resistance gene diversity of wheat breeding materials, and the markers developed here will permit further tracing of heterosomal chromosome fragments in the future.

Construction of a High-Density Genetic Map Based on SLAF Markers and QTL Analysis of Leaf Size in Rice

Leaf shape is an important agronomic trait for constructing an ideal plant type in rice, and high-density genetic map is facilitative in improving accuracy and efficiency for quantitative trait loci (QTL) analysis of leaf trait. In this study, a high-density genetic map contained 10,760 specific length amplified fragment sequencing (SLAF) markers was established based on 149 recombinant inbred lines (RILs) derived from the cross between Rekuangeng (RKG) and Taizhong1 (TN1), which exhibited 1,613.59 cM map distance with an average interval of 0.17 cM. A total of 24 QTLs were detected and explained the phenotypic variance ranged from 9% to 33.8% related to the leaf morphology across two areas. Among them, one uncloned major QTL qTLLW1 (qTLL1 and qTLLW1) involved in regulating leaf length and leaf width with max 33.8% and 22.5% phenotypic variance respectively was located on chromosome 1, and another major locus qTLW4 affecting leaf width accounted for max 25.3% phenotypic variance was mapped on chromosome 4. Fine mapping and qRT-PCR expression analysis indicated that qTLW4 may be allelic to NAL1 (Narrow leaf 1) gene.

Characterization of a wheat-tetraploid Thinopyrum elongatum 1E(1D) substitution line K17-841-1 by cytological and phenotypic analysis and developed molecular markers

Background

Tetraploid Thinopyrum elongatum (2n = 4x = 28) is a promising source of useful genes, including those related to adaptability and resistance to diverse biotic (Fusarium head blight, rust, powdery mildew, and yellow dwarf virus) and abiotic (cold, drought, and salt) stresses. However, gene transfer rates are low for this species and relatively few species-specific molecular markers are available.

Results

The wheat-tetraploid Th. elongatum line K17–841-1 derived from a cross between a hexaploid Trititrigia and Sichuan wheat cultivars was characterized based on sequential genomic and fluorescence in situ hybridizations and simple sequence repeat markers. We revealed that K17–841-1 is a 1E (1D) chromosomal substitution line that is highly resistant to stripe rust pathogen strains prevalent in China. By comparing the sequences generated during genotyping-by-sequencing (GBS), we obtained 597 specific fragments on the 1E chromosome of tetraploid Th. elongatum. A total of 235 primers were designed and 165 new Th. elongatum-specific markers were developed, with an efficiency of up to 70%. Marker validation analyses indicated that 25 specific markers can discriminate between the tetraploid Th. elongatum chromosomes and the chromosomes of other wheat-related species. An evaluation of the utility of these markers in a F₂ breeding population suggested these markers are linked to the stripe rust resistance gene on chromosome 1E. Furthermore, 28 markers are unique to diploid Th. elongatum, tetraploid Th. elongatum, or decaploid Thinopyrum ponticum, which carry the E genome. Finally, 48 and 74 markers revealed polymorphisms between Thinopyrum E-genome- containing species and Thinopyrum bessarabicum (E^b) and Pseudoroegneria libanotica (St), respectively.

Conclusions

This new substitution line provide appropriate bridge–breeding–materials for alien gene introgression to improve wheat stripe rust resistance. The markers developed using GBS technology in this study may be useful for the high-throughput and accurate detection of tetraploid Th. elongatum DNA in diverse materials. They may also be relevant for investigating the genetic differences and phylogenetic relationships among E, E^b, St, and other closely-related genomes and for further characterizing these complex species.

Molecular Analysis of Evolution and Origins of Cultivated Hawthorn (Crataegus spp.) and Related Species in China

Hawthorn is of high economic value owing to its medicinal properties and health benefits. Crataegus is a member of the Rosaceae family; the genus has a complicated taxonomic history, and several theories on its origin have been proposed. In this study, 53 accessions from seven Crataegus taxa native to China and accessions of exotic Crataegus species (two from Europe and one from North America) were analyzed by specific locus amplified fragment sequencing (SLAF-seq). In total, 933,450 single-nucleotide polymorphisms were identified after filtering and used to investigate the species' genomic evolution. Phylogenetic trees derived from nuclear simple sequence repeats (SSRs) and SLAF-seq data showed the same topology, in which Crataegus maximowiczii and Crataegus sanguineae formed a closely related cluster that was clearly separated from the cluster composed of Crataegus hupehensis, Crataegus pinnatifida, Crataegus pinnatifida var. major, Crataegus bretschneideri and Crataegus scabrifolia. Phylogenetic and structure analysis indicated that the seven Chinese Crataegus taxa had two separate speciation events. Plants that evolved the southwestern route shared the genepool with the European species, whereas plants along the northeastern route shared the genepool with the North American species. TreeMix genetic analysis revealed that C. bretschneideri may have a hybrid origin. This study provides valuable information on the origins of Chinese Crataegus and suggests an evolutionary model for the main Crataegus species that native to China.

From markers to genome-based breeding in wheat

Recent technological advances in wheat genomics provide new opportunities to uncover genetic variation in traits of breeding interest and enable genome-based breeding to deliver wheat cultivars for the projected food requirements for 2050. There has been tremendous progress in development of whole-genome sequencing resources in wheat and its progenitor species during the last 5 years. High-throughput genotyping is now possible in wheat not only for routine gene introgression but also for high-density genome-wide genotyping. This is a major transition phase to enable genome-based breeding to achieve progressive genetic gains to parallel to projected wheat production demands. These advances have intrigued wheat researchers to practice less pursued analytical approaches which were not practiced due to the short history of genome sequence availability. Such approaches have been successful in gene discovery and breeding applications in other crops and animals for which genome sequences have been available for much longer. These strategies include, (i) environmental genome-wide association studies in wheat genetic resources stored in genbanks to identify genes for local adaptation by using agroclimatic traits as phenotypes, (ii) haplotype-based analyses to improve the statistical power and resolution of genomic selection and gene mapping experiments, (iii) new breeding strategies for genome-based prediction of heterosis patterns in wheat, and (iv) ultimate use of genomics information to develop more efficient and robust genome-wide genotyping platforms to precisely predict higher yield potential and stability with greater precision. Genome-based breeding has potential to achieve the ultimate objective of ensuring sustainable wheat production through developing high yielding, climate-resilient wheat cultivars with high nutritional quality.

Development of High-Density SNP Markers and Their Application in Evaluating Genetic Diversity and Population Structure in Elaeis guineensis

High-density single nucleotide polymorphisms (SNPs) are used as highly favored makers to analyze genetic diversity and population structure, to construct high-density genetic maps and provide genotypes for genome-wide association analysis. In order to develop genome-wide SNP markers in oil palm (Elaeis guineensis), single locus amplified fragment sequencing (SLAF-seq) technology was performed in a diversity panel of 200 oil palm individuals and 1,261,501 SNPs were identified with minor allele frequency > 0.05 and integrity > 1. Among them, only 17.81% can be mapped within the genic region and the remaining was located into the intergenic region. A positive correlation was detected between the distribution of SNP markers and retrotransposons [transposable elements (TEs)]. Population structure analysis showed that the 200 individuals of oil palm can be divided into five subgroups based on cross-validation errors. However, the subpopulations divided for the 200 oil palm individuals based on the SNP markers were not accurately related to their geographical origins and 80 oil palm individuals from Malaysia showed highest genetic diversity. In addition, the physical distance of linkage disequilibrium (LD) decay in the analyzed oil palm population was 14.516 kb when r² = 0.1. The LD decay distances for different chromosomes varied from 3.324 (chromosome 15) to 19.983 kb (chromosome 7). Our research provides genome-wide SNPs for future targeted breeding in palm oil.

Identification of COS markers specific for Thinopyrum elongatum chromosomes preliminary revealed high level of macrosyntenic relationship between the wheat and Th. elongatum genomes

Thinopyrum elongatum (Host) D.R. Dewey has served as an important gene source for wheat breeding improvement for many years. The exact characterization of its chromosomes is important for the detailed analysis of prebreeding materials produced with this species. The major aim of this study was to identify and characterize new molecular markers to be used for the rapid analysis of E genome chromatin in wheat background. Sixty of the 169 conserved orthologous set (COS) markers tested on diverse wheat-Th. elongatum disomic/ditelosomic addition lines were assigned to various Th. elongatum chromosomes and will be used for marker-assisted selection. The macrosyntenic relationship between the wheat and Th. elongatum genomes was investigated using EST sequences. Several rearrangements were revealed in homoeologous chromosome groups 2, 5, 6 and 7, while chromosomes 1 and 4 were conserved. Molecular cytogenetic and marker analysis showed the presence of rearranged chromosome involved in 6ES and 2EL arms in the 6E disomic addition line. The selected chromosome arm-specific COS markers will make it possible to identify gene introgressions in breeding programmes and will also be useful in the development of new chromosome-specific markers, evolutionary analysis and gene mapping.

BrRLP48, Encoding a Receptor-Like Protein, Involved in Downy Mildew Resistance in Brassica rapa

Downy mildew, caused by Hyaloperonospora parasitica, is a major disease of Brassica rapa that causes large economic losses in many B. rapa-growing regions of the world. The genotype used in this study was based on a double haploid population derived from a cross between the Chinese cabbage line BY and a European turnip line MM, susceptible and resistant to downy mildew, respectively. We initially located a locus Br-DM04 for downy mildew resistance in a region about 2.7 Mb on chromosome A04, which accounts for 22.3% of the phenotypic variation. Using a large F₂ mapping population (1156 individuals) we further mapped Br-DM04 within a 160 kb region, containing 17 genes encoding proteins. Based on sequence annotations for these genes, four candidate genes related to disease resistance, BrLRR1, BrLRR2, BrRLP47, and BrRLP48 were identified. Overexpression of both BrRLP47 and BrRLP48 using a transient expression system significantly enhanced the downy mildew resistance of the susceptible line BY. But only the leaves infiltrated with RNAi construct of BrRLP48 could significantly reduce the disease resistance in resistant line MM. Furthermore, promoter sequence analysis showed that one salicylic acid (SA) and two jasmonic acid-responsive transcript elements were found in BrRLP48 from the resistant line, but not in the susceptible one. Real-time PCR analysis showed that the expression level of BrRLP48 was significantly induced by inoculation with downy mildew or SA treatment in the resistant line MM. Based on these findings, we concluded that BrRLP48 was involved in disease resistant response and the disease-inducible expression of BrRLP48 contributed to the downy mildew resistance. These findings led to a new understanding of the mechanisms of resistance and lay the foundation for marker-assisted selection to improve downy mildew resistance in Brassica rapa.

Physical mapping of the blue-grained gene from Thinopyrum ponticum chromosome 4Ag and development of blue-grain-related molecular markers and a FISH probe based on SLAF-seq technology

A Thinopyrum ponticum chromosome 4Ag physical map was constructed, the blue-grained gene was localized, and related specific markers and a FISH probe were developed by SLAF-seq. Decaploid Thinopyrum ponticum (2n = 10x = 70) serves as an important gene pool for wheat improvement. The wheat-Th. ponticum 4Ag (4D) disomic substitution line Blue 58, derived from a distant hybridization between Th. ponticum and common wheat (Triticum aestivum L.), bears blue coloration in the aleurone layer. To map the blue-grained gene, eight wheat-Th. ponticum 4Ag translocation lines with different chromosomal segment sizes were obtained from Blue 58 using ⁶⁰Co-γ ray irradiation and were characterized using cytogenetic and molecular marker analysis. A small-segment blue-grained wheat translocation line L13, accounting for one-fifth of 4AgL, was obtained. A physical map of chromosome 4Ag was constructed containing 573 specific-locus amplified fragment sequencing (SLAF-seq) markers, including three bins with 223 markers on 4AgS and eight bins with 350 markers on 4AgL. The blue-grained gene in three blue-grained translocation lines L5, L9, and L13, was located on bin 4AgL-6 with FL 0.75-0.89. Moreover, 89 blue-grain-related molecular markers and one fluorescence in situ hybridization (FISH) probe, pThp12.19, were identified in this bin. The newly developed translocation lines and the molecular markers and FISH probe will facilitate the application of the Th. ponticum-origin blue-grained characteristic in wheat breeding.

FISH-Based Markers Enable Identification of Chromosomes Derived From Tetraploid Thinopyrum elongatum in Hybrid Lines

Tetraploid Thinopyrum elongatum, which has superior abiotic stress tolerance characteristics, and exhibits resistance to stripe rust, powdery mildew, and Fusarium head blight, is a wild relative of wheat and a promising source of novel genes for wheat improvement. Currently, a high-resolution Fluorescence in situ hybridization (FISH) karyotype of tetraploid Th. elongatum is not available. To develop chromosome-specific FISH-based markers, the hexaploid Trititrigia 8801 and two accessions of tetraploid Th. elongatum were characterized by different repetitive sequences probes. We found that all E-genome chromosomes could be unambiguously identified using a combination of pSc119.2, pTa535, pTa71, and pTa713 repeats, and the E-genome chromosomes of the wild accessions and the partial amphiploid failed to exhibit any significant variation in the probe hybridization patterns. To verify the validation of these markers, the chromosome constitution of eight wheat- Th. elongatum hybrid derivatives were analyzed. We revealed that these probes could quickly detect wheat and tetraploid Th. elongatum chromosomes in hybrid lines. K16-712-1-2 was a 1E (1D) chromosome substitution line, K16-681-4 was a 2E disomic chromosome addition line, K16-562-3 was a 3E, 4E (3D, 4D) chromosome substitution line, K15-1033-8-2 contained one 4E, two 5E, and one 4ES⋅1DL Robertsonian translocation chromosome, and four other lines carried monosomic 4E, 5E, 6E, and 7E chromosome, respectively. Furthermore, the E-genome specific molecular markers analysis corresponded perfectly with the FISH results. The developed FISH markers will facilitate rapid identification of tetraploid Th. elongatum chromosomes in wheat improvement programs and allow appropriate alien chromosome transfer.

Development of Thinopyrum ponticum-specific molecular markers and FISH probes based on SLAF-seq technology

Based on SLAF-seq, 67 Thinopyrum ponticum-specific markers and eight Th. ponticum-specific FISH probes were developed, and these markers and probes could be used for detection of alien chromatin in a wheat background. Decaploid Thinopyrum ponticum (2n = 10x = 70) is a valuable gene reservoir for wheat improvement. Identification of Th. ponticum introgression would facilitate its transfer into diverse wheat genetic backgrounds and its practical utilization in wheat improvement. Based on specific-locus-amplified fragment sequencing (SLAF-seq) technology, 67 new Th. ponticum-specific molecular markers and eight Th. ponticum-specific fluorescence in situ hybridization (FISH) probes have been developed from a tiny wheat-Th. ponticum translocation line. These newly developed molecular markers allowed the detection of Th. ponticum DNA in a variety of materials specifically and steadily at high throughput. According to the hybridization signal pattern, the eight Th. ponticum-specific probes could be divided into two groups. The first group including five dispersed repetitive sequence probes could identify Th. ponticum chromatin more sensitively and accurately than genomic in situ hybridization (GISH). Whereas the second group having three tandem repetitive sequence probes enabled the discrimination of Th. ponticum chromosomes together with another clone pAs1 in wheat-Th. ponticum partial amphiploid Xiaoyan 68.

Wheat genetic resources in the post-genomics era: promise and challenges

Background

Wheat genetic resources have been used for genetic improvement since 1876, when Stephen Wilson (Transactions and Proceedings of the Botanical Society of Edinburgh 12: 286) consciously made the first wide hybrid involving wheat and rye in Scotland. Wide crossing continued with sporadic attempts in the first half of 19th century and became a sophisticated scientific discipline during the last few decades with considerable impact in farmers' fields. However, a large diversity of untapped genetic resources could contribute in meeting future wheat production challenges.

Perspectives and Conclusion

Recently the complete reference genome of hexaploid (Chinese Spring) and tetraploid (Triticum turgidum ssp. dicoccoides) wheat became publicly available coupled with on-going international efforts on wheat pan-genome sequencing. We anticipate that an objective appraisal is required in the post-genomics era to prioritize genetic resources for use in the improvement of wheat production if the goal of doubling yield by 2050 is to be met. Advances in genomics have resulted in the development of high-throughput genotyping arrays, improved and efficient methods of gene discovery, genomics-assisted selection and gene editing using endonucleases. Likewise, ongoing advances in rapid generation turnover, improved phenotyping, envirotyping and analytical methods will significantly accelerate exploitation of exotic genes and increase the rate of genetic gain in breeding. We argue that the integration of these advances will significantly improve the precision and targeted identification of potentially useful variation in the wild relatives of wheat, providing new opportunities to contribute to yield and quality improvement, tolerance to abiotic stresses, resistance to emerging biotic stresses and resilience to weather extremes.

Cytogenetics and stripe rust resistance of wheat-Thinopyrum elongatum hybrid derivatives

BACKGROUND

Amphidiploids generated by distant hybridization are commonly used as genetic bridge to transfer desirable genes from wild wheat species into cultivated wheat. This method is typically used to enhance the resistance of wheat to biotic or abiotic stresses, and to increase crop yield and quality. Tetraploid Thinopyrum elongatum exhibits strong adaptability, resistance to stripe rust and Fusarium head blight, and tolerance to salt, drought, and cold.

RESULTS

In the present study, we produced hybrid derivatives by crossing and backcrossing the Triticum durum-Th. elongatum partial amphidiploid (Trititrigia 8801, 2n = 6× = 42, AABBEE) with wheat cultivars common to the Sichuan Basin. By means of cytogenetic and disease resistance analyses, we identified progeny harboring alien chromosomes and measured their resistance to stripe rust. Hybrid progenies possessed chromosome numbers ranging from 40 to 47 (mean = 42.72), with 40.0% possessing 42 chromosomes. Genomic in situ hybridization revealed that the number of alien chromosomes ranged from 1 to 11. Out of the 50 of analyzed lines, five represented chromosome addition (2n = 44 = 42 W + 2E) and other five were chromosome substitution lines (2n = 42 = 40 W + 2E). Importantly, a single chromosome derived from wheat-Th. elongatum intergenomic Robertsonian translocations chromosome was occurred in 12 lines. Compared with the wheat parental cultivars ('CN16' and 'SM482'), the majority (70%) of the derivative lines were highly resistant to strains of stripe rust pathogen known to be prevalent in China.

CONCLUSION

The findings suggest that these hybrid-derivative lines with stripe rust resistance could potentially be used as germplasm sources for further wheat improvement.

Cytogenetic mapping of a major locus for resistance to Fusarium head blight and crown rot of wheat on Thinopyrum elongatum 7EL and its pyramiding with valuable genes from a Th. ponticum homoeologous arm onto bread wheat 7DL

A major locus for resistance to different Fusarium diseases was mapped to the most distal end of Th. elongatum 7EL and pyramided with Th. ponticum beneficial genes onto wheat 7DL. Perennial Triticeae species of the Thinopyrum genus are among the richest sources of valuable genes/QTL for wheat improvement. One notable and yet unexploited attribute is the exceptionally effective resistance to a major wheat disease worldwide, Fusarium head blight, associated with the long arm of Thinopyrum elongatum chromosome 7E (7EL). We targeted the transfer of the temporarily designated Fhb-7EL locus into bread wheat, pyramiding it with a Th. ponticum 7el₁L segment stably inserted into the 7DL arm of wheat line T4. Desirable genes/QTL mapped along the T4 7el₁L segment determine resistance to wheat rusts (Lr19, Sr25) and enhancement of yield-related traits. Mapping of the Fhb-7EL QTL, prerequisite for successful pyramiding, was established here on the basis of a bioassay with Fusarium graminearum of different 7EL-7el₁L bread wheat recombinant lines. These were obtained without resorting to any genetic pairing promotion, but relying on the close 7EL-7el₁L homoeology, resulting in 20% pairing frequency between the two arms. Fhb-7EL resided in the telomeric portion and resistant recombinants could be isolated with useful combinations of more proximally located 7el₁L genes/QTL. The transferred Fhb-7EL locus was shown to reduce disease severity and fungal biomass in grains of infected recombinants by over 95%. The same Fhb-7EL was, for the first time, proved to be effective also against F. culmorum and F. pseudograminearum, predominant agents of crown rot. Prebreeding lines possessing a suitable 7EL-7el₁L gene/QTL assembly showed very promising yield performance in preliminary field tests.

Rapid Development and Characterization of Chromosome Specific Translocation Line of Thinopyrum elongatum with Improved Dough Strength

The protein content and its type are principal factors affecting wheat (Triticum aestivum) end product quality. Among the wheat proteins, glutenin proteins, especially, high molecular weight glutenin subunits (HMW-GS) are major determinants of processing quality. Wheat and its primary gene pool have limited variation in terms of HMW-GS alleles. Wild relatives of wheat are an important source of genetic variation. For improvement of wheat processing quality its wild relative Thinopyrum elongatum with significant potential was utilized. An attempt was made to replace Th. elongatum chromosome long arm (1EL) carrying HMW-GS genes related to high dough strength with chromosome 1AL of wheat with least or negative effect on dough strength while retaining the chromosomes 1DL and 1BL with a positive effect on bread making quality. To create chromosome specific translocation line [1EL(1AS)], double monosomic of chromosomes 1E and 1A were created and further crossed with different cultivars and homoeologous pairing suppressor mutant line PhI . The primary selection was based upon glutenin and gliadin protein profiles, followed by sequential genomic in situ hybridization (GISH) and fluorescent in situ hybridization (FISH). These steps significantly reduced time, efforts, and economic cost in the generation of translocation line. In order to assess the effect of translocation on wheat quality, background recovery was carried out by backcrossing with recurrent parent for several generations and then selfing while selecting in each generation. Good recovery of parent background indicated the development of almost near isogenic line (NIL). Morphologically also translocation line was similar to recipient cultivar N61 that was further confirmed by seed storage protein profiles, RP-HPLC and scanning electron microscopy. The processing quality characteristics of translocation line (BC4F6) indicated significant improvement in the gluten performance index (GPI), dough mixing properties, dough strength, and extensibility. Our work aims to address the challenge of limited genetic diversity especially at chromosome 1A HMW-GS locus. We report successful development of chromosome 1A specific translocation line of Th. elongatum in wheat with improved dough strength.

A High Density Genetic Map Derived from RAD Sequencing and Its Application in QTL Analysis of Yield-Related Traits in Vigna unguiculata

Cowpea [Vigna unguiculata (L.) Walp.] is an annual legume of economic importance and widely grown in the semi-arid tropics. However, high-density genetic maps of cowpea are still lacking. Here, we identified 34,868 SNPs (single nucleotide polymorphisms) that were distributed in the cowpea genome based on the RAD sequencing (restriction-site associated DNA sequencing) technique using a population of 170 individuals (two cowpea parents and 168 F_2:3 progenies). Of these, 17,996 reliable SNPs were allotted to 11 consensus linkage groups (LGs). The length of the genetic map was 1,194.25 cM in total with a mean distance of 0.066 cM/SNP marker locus. Using this map and the F_2:3 population, combined with the CIM (composite interval mapping) method, eleven quantitative trait loci (QTL) of yield-related trait were detected on seven LGs (LG4, 5, 6, 7, 9, 10, and 11) in cowpea. These QTL explained 0.05-17.32% of the total phenotypic variation. Among these, four QTL were for pod length, four QTL for thousand-grain weight (TGW), two QTL for grain number per pod, and one QTL for carpopodium length. Our results will provide a foundation for understanding genes related to grain yield in the cowpea and genus Vigna.

Chromosome identification by new molecular markers and genomic in situ hybridization in the Triticum-Secale-Thinopyrum trigeneric hybrids

It is very important to use chromosome-specific markers for identifying alien chromosomes in advanced generations of distant hybridization. The chromosome-specific markers of rye and Thinopyrum elongatum, as well as genomic in situ hybridization, were used to identify the alien chromosomes in eight lines that were derived from the crossing between Triticum trititrigia (AABBEE) and triticale (AABBRR). The results showed that four lines contained all rye chromosomes but no Th. elongatum chromosomes. The line RE36-1 contained all of the rye chromosomes except for chromosome 2R. The lines RE33-2 and RE62-1 contained all rye chromosomes and 1E and 5E translocated chromosome, respectively. The line RE24-4 contained 12 rye chromosomes plus a 7E chromosome or 12 rye chromosomes plus one R-E translocated chromosome. Chromosome identification in the above lines was consistent using chromosome-specific markers and genomic in situ hybridization. These chromosome-specific markers provide useful tools for detecting alien chromosomes in trigeneric hybrids, and these lines could be utilized as valuable germplasm in wheat improvement.

Molecular Cytogenetic Characterization of two Triticum-Secale-Thinopyrum Trigeneric Hybrids Exhibiting Superior Resistance to Fusarium Head Blight, Leaf Rust, and Stem Rust Race Ug99

Fusarium head blight (FHB), leaf rust, and stem rust are the most destructive fungal diseases in current world wheat production. The diploid wheatgrass, Thinopyrum elongatum (Host) Dewey (2n = 2x = 14, EE) is an excellent source of disease resistance genes. Two new Triticum-Secale-Thinopyrum trigeneric hybrids were derived from a cross between a hexaploid triticale (X Triticosecale Wittmack, 2n = 6x = 42, AABBRR) and a hexaploid Triticum trititrigia (2n = 6x = 42, AABBEE), were produced and analyzed using genomic in situ hybridization and molecular markers. The results indicated that line RE21 contained 14 A-chromosomes, 14 B-chromosomes, three pairs of R-chromosomes (4R, 6R, and 7R), and four pairs of E-chromosomes (1E, 2E, 3E, and 5E) for a total chromosome number of 2n = 42. Line RE62 contained 14 A-chromosomes, 14 B-chromosomes, six pairs of R-chromosomes, and one pair of translocation chromosomes between chromosome 5R and 5E, for a total chromosome number of 2n = 42. At the seedling and adult growth stages under greenhouse conditions, line RE21 showed high levels of resistance to FHB, leaf rust, and stem rust race Ug99, and line RE62 was highly resistant to leaf rust and stem rust race Ug99. These two lines (RE21 and RE62) display superior disease resistance characteristics and have the potential to be utilized as valuable germplasm sources for future wheat improvement.

Genome-Wide SNP Markers Based on SLAF-Seq Uncover Breeding Traces in Rapeseed (Brassica napus L.)

Single Nucleotide Polymorphisms (SNPs) are the most abundant and richest form of genomic polymorphism, and hence make highly favorable markers for genetic map construction and genome-wide association studies. In this study, a total of 300 rapeseed accessions (278 representative of Chinese germplasm, plus 22 outgroup accessions of different origins and ecotypes) were collected and sequenced using Specific-Locus Amplified Fragment Sequencing (SLAF-seq) technology, obtaining 660.25M reads with an average sequencing depth of 6.27 × and a mean Q30 of 85.96%. Based on the 238,711 polymorphic SLAF tags a total of 1,197,282 SNPs were discovered, and a subset of 201,817 SNPs with minor allele frequency >0.05 and integrity >0.8 were selected. Of these, 30,877 were designated SNP "hotspots," and 41 SNP-rich genomic regions could be delineated, with 100 genes associated with plant resistance, vernalization response, and signal transduction detected in these regions. Subsequent analysis of genetic diversity, linkage disequilibrium (LD), and population structure in the 300 accessions was carried out based on the 201,817 SNPs. Nine subpopulations were observed based on the population structure analysis. Hierarchical clustering and principal component analysis divided the 300 varieties roughly in accordance with their ecotype origins. However, spring-type varieties were intermingled with semi-winter type varieties, indicating frequent hybridization between spring and semi-winter ecotypes in China. In addition, LD decay across the whole genome averaged 299 kb when r² = 0.1, but the LD decay in the A genome (43 kb) was much shorter than in the C genome (1,455 kb), supporting the targeted introgression of the A genome from progenitor species B. rapa into Chinese rapeseed. This study also lays the foundation for genetic analysis of important agronomic traits using this rapeseed population.

Physical Location of New PCR-Based Markers and Powdery Mildew Resistance Gene(s) on Rye (Secale cereale L.) Chromosome 4 Using 4R Dissection Lines

Rye (Secale cereale L.) 4R chromosome contains elite genes that are applicable for wheat (Triticum aestivum L.) cultivar improvement. PCR-based 4R-specific markers can benefit the detection of elite genes on 4R in wheat backgrounds. In this study, a new fluorescence in situ hybridization (FISH) map of the 4R^Ku chromosome of rye Kustro has been constructed. A set of 4R^Ku dissection lines was obtained and 301 new 4R^Ku-specific markers were developed using specific length amplified fragment sequencing (SLAF-seq) technology. These markers were combined with the 99 4R^Ku-specific markers previously developed, and were physically mapped to 4R^Ku chromosome using the new FISH map and the 4R^Ku dissection lines. A total of 338 of the 400 markers have been successfully mapped to six regions of 4R^Ku chromosome. Additionally, the powdery mildew resistance gene(s) on the 4RL^Ku arm was located to the segment between L.4 and L.8, the same region where 115 4RL^Ku-specific markers were mapped. The markers developed in this study can be used to identify a specific segment of 4R chromatin in wheat backgrounds, help construct a high-density physical map of 4R chromosome, and facilitate the utilization of elite genes on 4R chromosome in wheat breeding programs.

Rapid identification of QTLs underlying resistance to Cucumber mosaic virus in pepper (Capsicum frutescens)

Next-generation sequencing enabled a fast discovery of QTLs controlling CMV resistant in pepper. The gene CA02g19570 as a possible candidate gene of qCmr2.1 was identified for resistance to CMV in pepper. Cucumber mosaic virus (CMV) is one of the most important viruses infecting pepper, but the genetic basis of CMV resistance in pepper is elusive. In this study, we identified a candidate gene for CMV resistance QTL, qCmr2.1 through SLAF-seq. Segregation analysis in F₂, BC₁ and F_2:3 populations derived from a cross between two inbred lines 'PBC688' (CMV-resistant) and 'G29' (CMV-susceptible) suggested quantitative inheritance of resistance to CMV in pepper. Genome-wide comparison of SNP profiles between the CMV-resistant and CMV-susceptible bulks constructed from an F₂ population identified two QTLs, designated as qCmr2.1 on chromosome 2 and qCmr11.1 on chromosome 11 for resistance to CMV in PBC688, which were confirmed by InDel marker-based classical QTL mapping in the F₂ population. As a major QTL, joint SLAF-seq and traditional QTL analysis delimited qCmr2.1 to a 330 kb genomic region. Two pepper genes, CA02g19570 and CA02g19600, were identified in this region, which are homologous with the genes LOC104113703, LOC104248995, LOC102603934 and LOC101248357, which were predicted to encode N-like protein associated with TMV-resistant in Solanum crops. Quantitative RT-PCR revealed higher expression levels of CA02g19570 in CMV resistance genotypes. The CA02g19600 did not exhibit obvious regularity in expression patterns. Higher relative expression levels of CA02g19570 in PBC688 and F₁ were compared with those in G29 during days after inoculation. These results provide support for CA02g19570 as a possible candidate gene of qCmr2.1 for resistance to CMV in pepper.

Genome-Wide SNP Markers Based on SLAF-Seq Uncover Breeding Traces in Rapeseed (Brassica napus L.)

Single Nucleotide Polymorphisms (SNPs) are the most abundant and richest form of genomic polymorphism, and hence make highly favorable markers for genetic map construction and genome-wide association studies. In this study, a total of 300 rapeseed accessions (278 representative of Chinese germplasm, plus 22 outgroup accessions of different origins and ecotypes) were collected and sequenced using Specific-Locus Amplified Fragment Sequencing (SLAF-seq) technology, obtaining 660.25M reads with an average sequencing depth of 6.27 × and a mean Q30 of 85.96%. Based on the 238,711 polymorphic SLAF tags a total of 1,197,282 SNPs were discovered, and a subset of 201,817 SNPs with minor allele frequency >0.05 and integrity >0.8 were selected. Of these, 30,877 were designated SNP "hotspots," and 41 SNP-rich genomic regions could be delineated, with 100 genes associated with plant resistance, vernalization response, and signal transduction detected in these regions. Subsequent analysis of genetic diversity, linkage disequilibrium (LD), and population structure in the 300 accessions was carried out based on the 201,817 SNPs. Nine subpopulations were observed based on the population structure analysis. Hierarchical clustering and principal component analysis divided the 300 varieties roughly in accordance with their ecotype origins. However, spring-type varieties were intermingled with semi-winter type varieties, indicating frequent hybridization between spring and semi-winter ecotypes in China. In addition, LD decay across the whole genome averaged 299 kb when r² = 0.1, but the LD decay in the A genome (43 kb) was much shorter than in the C genome (1,455 kb), supporting the targeted introgression of the A genome from progenitor species B. rapa into Chinese rapeseed. This study also lays the foundation for genetic analysis of important agronomic traits using this rapeseed population.

Chromosomal Localization of Genes Conferring Desirable Agronomic Traits from Wheat-Agropyron cristatum Disomic Addition Line 5113

Creation of wheat-alien disomic addition lines and localization of desirable genes on alien chromosomes are important for utilization of these genes in genetic improvement of common wheat. In this study, wheat-Agropyron cristatum derivative line 5113 was characterized by genomic in situ hybridization (GISH) and specific-locus amplified fragment sequencing (SLAF-seq), and was demonstrated to be a novel wheat-A. cristatum disomic 6P addition line. Compared with its parent Fukuhokomugi (Fukuho), 5113 displayed multiple elite agronomic traits, including higher uppermost internode/plant height ratio, larger flag leaf, longer spike length, elevated grain number per spike and spikelet number per spike, more kernel number in the middle spikelet, more fertile tiller number per plant, and enhanced resistance to powdery mildew and leaf rust. Genes conferring these elite traits were localized on the A. cristatum 6P chromosome by using SLAF-seq markers and biparental populations (F1, BC1F1 and BC1F2 populations) produced from the crosses between Fukuho and 5113. Taken together, chromosomal localization of these desirable genes will facilitate transferring of high-yield and high-resistance genes from A. cristatum into common wheat, and serve as the foundation for the utilization of 5113 in wheat breeding.

New molecular markers and cytogenetic probes enable chromosome identification of wheat-Thinopyrum intermedium introgression lines for improving protein and gluten contents

New molecular markers were developed for targeting Thinopyrum intermedium 1St#2 chromosome, and novel FISH probe representing the terminal repeats was produced for identification of Thinopyrum chromosomes. Thinopyrum intermedium has been used as a valuable resource for improving the disease resistance and yield potential of wheat. A wheat-Th. intermedium ssp. trichophorum chromosome 1St#2 substitution and translocation has displayed superior grain protein and wet gluten content. With the aim to develop a number of chromosome 1St#2 specific molecular and cytogenetic markers, a high throughput, low-cost specific-locus amplified fragment sequencing (SLAF-seq) technology was used to compare the sequences between a wheat-Thinopyrum 1St#2 (1D) substitution and the related species Pseudoroegneria spicata (St genome, 2n = 14). A total of 5142 polymorphic fragments were analyzed and 359 different SLAF markers for 1St#2 were predicted. Thirty-seven specific molecular markers were validated by PCR from 50 randomly selected SLAFs. Meanwhile, the distribution of transposable elements (TEs) at the family level between wheat and St genomes was compared using the SLAFs. A new oligo-nucleotide probe named Oligo-pSt122 from high SLAF reads was produced for fluorescence in situ hybridization (FISH), and was observed to hybridize to the terminal region of 1St#L and also onto the terminal heterochromatic region of Th. intermedium genomes. The genome-wide markers and repetitive based probe Oligo-pSt122 will be valuable for identifying Thinopyrum chromosome segments in wheat backgrounds.

Identification and Validation of SNP Markers Linked to Dwarf Traits Using SLAF-Seq Technology in Lagerstroemia

The genetic control of plant architecture is a promising approach to breed desirable cultivars, particularly in ornamental flowers. In this study, the F1 population (142 seedlings) derived from Lagerstroemia fauriei (non-dwarf) × L. indica 'Pocomoke' (dwarf) was phenotyped for six traits (plant height (PH), internode length (IL), internode number, primary lateral branch height (PLBH), secondary lateral branch height and primary branch number), and the IL and PLBH traits were positively correlated with the PH trait and considered representative indexes of PH. Fifty non-dwarf and dwarf seedlings were pooled and subjected to a specific-locus amplified fragment sequencing (SLAF-seq) method, which screened 1221 polymorphic markers. A total of 3 markers segregating between bulks were validated in the F1 population, with the M16337 and M38412 markers highly correlated with the IL trait and the M25207 marker highly correlated with the PLBH trait. These markers provide a predictability of approximately 80% using a single marker (M25207) and a predictability of 90% using marker combinations (M16337 + M25207) in the F1 population, which revealed that the IL and the PLBH traits, especially the PLBH, were the decisive elements for PH in terms of molecular regulation. Further validation was performed in the BC1 population and a set of 28 Lagerstroemia stocks using allele-specific PCR (AS-PCR) technology, and the results showed the stability and reliability of the SNP markers and the co-determination of PH by multiple genes. Our findings provide an important theoretical and practical basis for the early prediction and indirect selection of PH using the IL and the PLBH, and the detected SNPs may be useful for marker-assisted selection (MAS) in crape myrtle.

Construction of high-density genetic linkage map and identification of flowering-time QTLs in orchardgrass using SSRs and SLAF-seq

Orchardgrass (Dactylis glomerata L.) is one of the most economically important perennial, cool-season forage species grown and pastured worldwide. High-density genetic linkage mapping is a valuable and effective method for exploring complex quantitative traits. In this study, we developed 447,177 markers based on SLAF-seq and used them to perform a comparative genomics analysis. Perennial ryegrass sequences were the most similar (5.02%) to orchardgrass sequences. A high-density linkage map of orchardgrass was constructed using 2,467 SLAF markers and 43 SSRs, which were distributed on seven linkage groups spanning 715.77 cM. The average distance between adjacent markers was 0.37 cM. Based on phenotyping in four environments, 11 potentially significant quantitative trait loci (QTLs) for two target traits–heading date (HD) and flowering time (FT)–were identified and positioned on linkage groups LG1, LG3, and LG5. Significant QTLs explained 8.20–27.00% of the total phenotypic variation, with the LOD ranging from 3.85–12.21. Marker167780 and Marker139469 were associated with FT and HD at the same location (Ya’an) over two different years. The utility of SLAF markers for rapid generation of genetic maps and QTL analysis has been demonstrated for heading date and flowering time in a global forage grass.

Genome-wide association study of 8 carcass traits in Jinghai Yellow chickens using specific-locus amplified fragment sequencing technology

Carcass traits are important to the commercial chicken industry, and understanding the genetics of these traits will be useful in the development of commercially viable varieties of chickens. We conducted a genome-wide association study based on 8 carcass trait phenotypes in a population of 400 43-week-old Jinghai Yellow chickens. Specific-locus amplified fragment sequencing technology was used to identify 90,961 single nucleotide polymorphisms (SNP) distributed among 29 chromosomes and the mitochondrial genome. SNP that were significantly associated with phenotypic traits were identified by a simple general linear model. Fifteen SNP attained genome-wide significance (P < 1.87E−6) and were associated with 5 of the 8 carcass traits; only one SNP was significantly associated with 2 traits (foot weight and wing weight). Twelve genes were associated with these 15 SNP. A region of chromosome 4 between 75.5 and 76.1 Mb was associated with carcass weight, foot weight, and wing weight. An 84-kb region on chromosome 3 (51.2 Mb) was associated with eviscerated weight and semi-eviscerated weight.