In crop plants, a high-density genetic linkage map is essential for both genetic and genomic researches. The complexity and the large size of wheat genome have hampered the acquisition of a high-resolution genetic map. In this study, we report a high-density genetic map based on an individual mapping population using the Affymetrix Wheat660K single-nucleotide polymorphism (SNP) array as a probe in hexaploid wheat. The resultant genetic map consisted of 119 566 loci spanning 4424.4 cM, and 119 001 of those loci were SNP markers. This genetic map showed good collinearity with the 90 K and 820 K consensus genetic maps and was also in accordance with the recently released wheat whole genome assembly. The high-density wheat genetic map will provide a major resource for future genetic and genomic research in wheat. Moreover, a comparative genomics analysis among gramineous plant genomes was conducted based on the high-density wheat genetic map, providing an overview of the structural relationships among theses gramineous plant genomes. A major stable quantitative trait locus (QTL) for kernel number per spike was characterized, providing a solid foundation for the future high-resolution mapping and map-based cloning of the targeted QTL.

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Utilization of a Wheat660K SNP array-derived high-density genetic map for high-resolution mapping of a major QTL for kernel number

Two wheat–Thinopyrum substitution lines X479 and X482 selected from the progenies of wheat “Mianyang26 (MY26)” × wheat–Thinopyrum intermedium ssp. trichophorum partial amphiploid were characterized by seed storage protein electrophoresis, genomic in situ hybridization (GISH), fluorescence in situ hybridization (FISH), and PCR-based molecular markers. Seed storage protein analysis showed that X479 expressed some of Th. intermedium ssp. trichophorum-specific gliadin and glutenin bands. Chromosome counting and GISH probed by Pseudoroegneria spicata genomic DNA indicated that two pairs of Thinopyrum-derived chromosomes (St genome and St–JS translocated chromosomes) substituted for two pairs of wheat chromosomes in both X479 and X482. FISH using pAs1 and pHvG38 as probes showed that chromosomes 1B and 4B, and 4D and 6D were absent in X479 and X482, respectively. Using the newly isolated JS chromosome-specific repetitive sequence pDb12H as a probe, the FISH signals revealed that the translocation of St–JS chromosomes in X479 and X482 occurred in repetitive sequence regions of the short arm. The molecular markers based on wheat–rice colinearity confirmed that the chromosome constitutions of X479 and X482 were 1St (1B) + 4St–4JS (4B) and 4St–JS (4D) + 6St (6D), respectively. The substitution lines were both fully fertile which suggests that the Th. intermedium chromosomes in X479 and X482 substitute well for the corresponding wheat chromosomes. The rust resistance and novel agronomic traits revealed that the substitution lines will be potentially useful for genetic improvement of wheat.

Precise identification of two wheat–Thinopyrum intermedium substitutions reveals the compensation and rearrangement between wheat and Thinopyrum chromosomes

Genetic improvement of soybean protein meal is a complex process because of negative correlation with oil, yield, and temperature. This review describes the progress in mapping and genomics, identifies knowledge gaps, and highlights the need of integrated approaches.
 Meal protein derived from soybean [Glycine max (L) Merr.] seed is the primary source of protein in poultry and livestock feed. Protein is a key factor that determines the nutritional and economical value of soybean. Genetic improvement of soybean seed protein content is highly desirable, and major quantitative trait loci (QTL) for soybean protein have been detected and repeatedly mapped on chromosomes (Chr.) 20 (LG-I), and 15 (LG-E). However, practical breeding progress is challenging because of seed protein content’s negative genetic correlation with seed yield, other seed components such as oil and sucrose, and interaction with environmental effects such as temperature during seed development. In this review, we discuss rate-limiting factors related to soybean protein content and nutritional quality, and potential control factors regulating seed storage protein. In addition, we describe advances in next-generation sequencing technologies for precise detection of natural variants and their integration with conventional and high-throughput genotyping technologies. A syntenic analysis of QTL on Chr. 15 and 20 was performed. Finally, we discuss comprehensive approaches for integrating protein and amino acid QTL, genome-wide association studies, whole-genome resequencing, and transcriptome data to accelerate identification of genomic hot spots for allele introgression and soybean meal protein improvement.

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Molecular mapping and genomics of soybean seed protein: a review and perspective for the future.

The last decade has been characterized by a decrease in peach (Prunus persica) fruit consumption in many countries, foremost due to unsatisfactory quality. The sugar content is one of the most important quality traits perceived by consumers, and the development of novel peach cultivars with sugar-enhanced content is a primary objective of breeding programs to revert the market inertia. Nevertheless, the progress reachable through classical phenotypic selection is limited by the narrow genetic bases of peach breeding material and by the complex quantitative nature of the trait, which is deeply affected by environmental conditions and agronomical management. The development of molecular markers applicable in MAS or MAB has become an essential strategy to boost the selection efficiency. Despite the enormous advances in 'omics' sciences, providing powerful tools for plant genotyping, the identification of the genetic bases of sugar-related traits is hindered by the lack of adequate phenotyping methods that are able to address strong within-plant variability. This review provides an overview of the current knowledge of the metabolic pathways and physiological mechanisms regulating sugar accumulation in peach fruit, the main advances in phenotyping approaches and genetic background, and finally addressing new research priorities and prospective for breeders.

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Sugars in peach fruit: a breeding perspective

Sweetness is one of the main drivers of consumer preference, and thus is given high priority in apple breeding programmes. Due to the complexity of sweetness evaluation, soluble solid content (SSC) is commonly used as an estimation of this trait. Nevertheless, it has been demonstrated that SSC and sweet taste are poorly correlated. Though individual sugar content may vary greatly between and within apple cultivars, no previous study has tried to investigate the relationship between the amount of individual sugars, or ratios of these, and apple sweetness. In this work, we quantified the major sugars (sucrose, glucose, fructose, xylose) and sorbitol and explored their influence on perceived sweetness in apple; we also related this to malic acid content, SSC and volatile compounds. Our data confirmed that the correlation between sweetness and SSC is weak. We found that sorbitol content correlates (similarly to SSC) with perceived sweetness better than any other single sugar or total sugar content. The single sugars show no differentiable importance in determining apple sweetness. Our predictive model based on partial least squares regression shows that after sorbitol and SSC, the most important contribution to apple sweetness is provided by several volatile compounds, mainly esters and farnesene.

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Sweet taste in apple: the role of sorbitol, individual sugars, organic acids and volatile compounds

Thinopyrum elongatum serves as an excellent gene pool for wheat improvement. Genes for resistance to many biotic and abiotic stresses have been transferred from Th. elongatum to wheat through chromosome manipulation. For breeding programs, molecular markers enable screening of a large number of genotypes for alien chromosome introgressions. The main objective of the present study was to develop and characterize EST (expressed sequence tags) and PLUG (PCR-based Landmark Unique Gene) markers that can distinguish Th. elongatum chromatin from the wheat genomes. A total of 258 mapped EST primer pairs and 46 PLUG primer pairs were tested on DNA from wheat Chinese Spring (CS) and CS-Th. elongatum addition lines. The results showed that 43 primer pairs could be effectively mapped to specific Th. elongatum chromosomes. Twenty-two of the 43 markers displayed similar homoeologous chromosome locations to hexaploid wheat. Nine markers mapped to different linkage groups between wheat and Th. elongatum, while 12 makers mapped on two or three different Th. elongatum chromosomes. A comparison of molecular marker locations indicated that Th. elongatum genome was closely related to the D genome of wheat, and chromosome rearrangements and duplication had occurred in Th. elongatum and the wheat genomes. The markers will be useful in comparative gene mapping, chromosome evolutionary analysis, and gene introgression for wheat improvement using Th. elongatum accessions as gene donors.

Genomic rearrangement between wheat and Thinopyrum elongatum revealed by mapped functional molecular markers

Stripe rust, caused by Puccinia striiformis f. sp. tritici, was one of the most disaster foliar diseases for wheat-growing areas of the world. Thinopyrum intermedium has provided novel resistance genes to multi-fungal disease, and new wheat-Th. intermedium derivatives for stripe rust resistance still need to develop for wheat breeding. Wheat line X484-3 was selected from a cross between wheat line MY11 and wheat-Th. intermedium ssp. trichophorum partial amphiploid TE-1508, and was characterized by genomic in situ hybridization (GISH) and functional molecular markers. Chromosome counting revealed that the X484-3 was 2n = 44 and GISH analysis using Pseudoroegneria spicata genomic DNAas a probe demonstrated that X484-3 contained a pair of St-chromosomes from Th. intermedium donor parents. The functional molecular markers confirmed that introduced St-chromosomes belonging to linkage group 7, indicating that line X484-3 was a 7St addition line. The resistance observation displayed that the introduced Th. intermedium ssp. trichophorum derived chromosomes 7St were responsible for the stripe rust resistances at adult plant. The identified wheat-Th. intermedium chromosome 7St addition line X484-3 can be used as a donor in wheat breeding for stripe rust resistance.

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Molecular identification of a new wheat-Thinopyrum intermedium ssp. trichophorum addition line for resistance to stripe rust

The tribe Triticeae provides a vast gene pool for most agronomically important traits, including some that do not exist in wheat. Species in the genus Dasypyrum, namely D. villosum andD. breviaristatum, are important sources for improving genetic variability of bread wheat (Liu et al. 2010). The genes for high seed protein, powdery mildew resistance, stripe rust resistance, eyespot resistance and spindle streak mosaic virus resistance were transferred from D. villosum to wheat (De Pace et al. 2011). To introduce novel disease resistance genes from tetraploidD. breviaristatum to bread wheat, we produced new molecular markers based on genomespecific centromeric retrotransposons which are effective for tracing Dasypyrum chromatin in wheat background. The retrotransposons are divided into long terminal repeat (LTR) retrotransposons and non-LTR retrotransposons, which are commonly found in cereal genomes (Jiang et al. 1996). LTR retrotransposons consist of two major groups, Ty1-copia and Ty3-gypsy. In cereal species, two families of repeats, CCS1 and pSau3A9, representing parts of a Ty3-gypsy-like retroelement, are conserved in the centromeric regions (Aragon-Alcaide et al. 1996; Jiang et al. 1996). The homologue of CCS1 and multiple copies of partial or complete Ty3-gypsy retrotransposons were identified and localized in the centromeric regions of barley and wheat genomes (Hudakova et al. 2001; Li et al. 2004). Besides the Triticeae conserved centromeric retrotransposon sequences, some species-specific centromere repeats had also been isolated from genera of Triticeae tribe, such as Secale and Pseudoroengeria (Francki 2001; Lu et al. 2009). The objective of the current study was to isolate a new centromeric Ty3-gypsy-like DNA sequence from D. breviaristatum, and investigate its chromosomal location in Dasypyrum

Xiao-Jin Song

Papers

Precise identification of two wheat–Thinopyrum intermedium substitutions reveals the compensation and rearrangement between wheat and Thinopyrum chromosomes

Genomic rearrangement between wheat and Thinopyrum elongatum revealed by mapped functional molecular markers

Molecular identification of a new wheat-Thinopyrum intermedium ssp. trichophorum addition line for resistance to stripe rust

Chromosomal distribution of a new centromeric Ty3-gypsy retrotransposon sequence in Dasypyrum and related Triticeae species