Shuiyang Yu

The draft genome of Tibetan hulless barley reveals adaptive patterns to the high stressful Tibetan Plateau

Significance The draft genome of Tibetan hulless barley provides a robust framework to better understand Poaceae evolution and a substantial basis for functional genomics of crop species with a large genome. The expansion of stress-related gene families in Tibetan hulless barley implies that it could be considered as an invaluable gene resource aiding stress tolerance improvement in Triticeae crops. Genome resequencing revealed extensive genetic diversity in Tibetan barley germplasm and divergence to sequenced barley genomes from other geographical regions. Investigation of genome-wide selection footprints demonstrated an adaptive correlation of genes under selection with extensive stressful environmental variables. These results reveal insights into the adaptation of Tibetan hulless barley to harsh environments on the highland and will facilitate future genetic improvement of crops. The Tibetan hulless barley (Hordeum vulgare L. var. nudum), also called “Qingke” in Chinese and “Ne” in Tibetan, is the staple food for Tibetans and an important livestock feed in the Tibetan Plateau. The diploid nature and adaptation to diverse environments of the highland give it unique resources for genetic research and crop improvement. Here we produced a 3.89-Gb draft assembly of Tibetan hulless barley with 36,151 predicted protein-coding genes. Comparative analyses revealed the divergence times and synteny between barley and other representative Poaceae genomes. The expansion of the gene family related to stress responses was found in Tibetan hulless barley. Resequencing of 10 barley accessions uncovered high levels of genetic variation in Tibetan wild barley and genetic divergence between Tibetan and non-Tibetan barley genomes. Selective sweep analyses demonstrate adaptive correlations of genes under selection with extensive environmental variables. Our results not only construct a genomic framework for crop improvement but also provide evolutionary insights of highland adaptation of Tibetan hulless barley.

Molecular detection of rye (Secale cereale L.) chromatin in wheat line 07jian126 (Triticum aestivum L.) and its association to wheat powdery mildew resistance

Powdery mildew (Pm), caused by Blumeria graminis f. sp. tritici (Bgt), is one of the most serious diseases for common wheat in many regions around the world. Seeking for new resistance source is urgently required to meet the challenge of the rapid loss of resistance due to the co-evolution of the pathogen’s virulence. Wheat line 07jian126 (Triticum aestivum L.) is highly resistant to the Pm disease prevailing in Sichuan province of China. Previous study showed that a SSR marker Xbarc183 was linked to the Pm resistance in 07jian126, which might be controlled by a single dominant gene, designated as Pm07J126. In this study, two additional F2 populations were used to confirm the linkage between Pm07J126 and Xbarc183. Furthermore, rye chromatin was detected in 07jian126 by molecular analysis of a rye-specific SCAR marker O5 which co-segregated with Pm07J126. This result indicated that Pm07J126 might originate from rye. The reaction patterns to 21 Bgt isolates and molecular marker analysis implied that Pm07J126 might be different from the known rye-derived Pm genes Pm7, Pm8, Pm17 and PmJZHM2RL. Chromosome observation, molecular marker, and A-PAGE analysis suggested that 07jian126 might be a rye introgression line and neither contain 1RS translocation nor secalins gene. Consequently, 07jian126 could be considered as a valuable resource for Pm resistance development of wheat. Besides, the molecular markers Xbarc183 and O5 are useful in marker-assisted selection of Pm07J126 in wheat breeding programs.

Characterization of a genome-specific Gypsy-like retrotransposon sequence and development of a molecular marker specific for Dasypyrum villosum (L.)

Triticum aestivum Chinese Spring (CS), Xiaoyan 54, Gaoyou 503, ABD Mianyang 26, Neimai 9, 9R178, 9R137 Dasypyrum villosum W67266, W67290, H.V078, H.V077, H.V076 V Triticum durum D311, Mo7, 81086A AB Secale cereale JZHM, 501 R Aegilops ventricosa As 106 DvDvMvMv Ae. uniaristata As136 M Ae. tauschii 38 D T. durum D. villosum amphipoild Th1w, Th2w, Th3w, Th1,Th3 ABV T. aestivum (CS) D. villorum additional lines Add.∗ 1V-7V ABDV

Localization of the powdery mildew resistance gene Pm07J126 in wheat (Triticum aestivum L.)

Powdery mildew (Pm), caused by Blumeria graminis f. sp. tritici (Bgt), is one of the most serious diseases of common wheat (Triticum aestivum L.) in many regions of the world. Rapid loss of resistance caused by pathogen virulence requires continual improvement of Pm resistance through utilization of novel resistance genes. Pm07J126, in wheat line 07jian126, is a dominant resistance gene, conferring immunity to the prevailing Bgt population in Sichuan province. Previous studies showed that Pm07J126 might be derived from rye (Secale cereale L.) and that it was closely linked with SSR marker barc183. In this study, we localized Pm07J126 to the distal end of chromosome 6DS based on markers barc183 and cfd135. Collinearity analysis of wheat, Brachypodium and rice helped to identify an sequence tagged site marker in close proximity to barc183 in chromosome bin 6DS6-0.99-1.00. Marker Xcib9 that co-segregated with Pm07J126 should be useful for marker-assisted selection in wheat breeding programs.

A Single Nucleotide Polymorphism of Nud Converts the Caryopsis Type of Barley (Hordeum Vulgare L.)

Whether the caryopsis of barley is naked or covered is controlled by the Nud gene encoding an ethylene response factor (ERF) family transcription factor (TF) of the AP2/ERF TF superfamily that is involved in the lipid biosynthesis pathway. In covered barley, lipids on the surface of caryopses act as a glue for their tight adhesion with hulls. Separation of hulls in naked barley is due to the absence of surface lipids on caryopses. A natural deletion event of Nud was found to be the determinant of naked caryopsis and had been proposed as the monophyletic origin of domesticated naked barley. In the present study, we re-sequenced the nud locus in 162 barleys, comprising 79 covered and 83 naked barleys varieties. Besides the normal deletion mutation of Nud contributing to naked caryopsis, we found a novel allele of Nud, designated as nud1.g, distinctly in three naked barleys collected from Tibet. nud1.g contains a non-synonymous SNP T643A when compared with the functional Nud gene. Genetic analysis indicated that the SNP T643A of nud1.g co-segregates with the naked phenotype. The nud1.g gene was expressed normally in the three naked barleys. Furthermore, in silico prediction of functionally conserved sites and 3D structures showed that the amino acid substitution (valine to aspartate) caused by SNP T643A may lead to a dramatic structural alteration of NUD that may result in loss of function. This study provides evidence of a new origin of the naked phenotype of domesticated barley in Tibet.