Whole-genome sequencing of diverse wheat accessions uncovers genetic changes during modern breeding in China and the United States.

Breeding has dramatically changed the plant architecture of wheat (Triticum aestivum), resulting in the development of high-yielding varieties adapted to modern farming systems. However, how wheat breeding shaped the genomic architecture of this crop remains poorly understood. Here, we performed a comprehensive comparative analysis of a whole-genome resequencing panel of 355 common wheat accessions (representing diverse landraces and modern cultivars from China and the United States) at the phenotypic and genomic levels. The genetic diversity of modern wheat cultivars was clearly reduced compared to landraces. Consistent with these genetic changes, most phenotypes of cultivars from China and the United States were significantly altered. Of the 21 agronomic traits investigated, 8 showed convergent changes between the 2 countries. Moreover, of the 207 loci associated with these 21 traits, more than half overlapped with genomic regions that showed evidence of selection. The distribution of selected loci between the Chinese and American cultivars suggests that breeding for increased productivity in these 2 regions was accomplished by pyramiding both shared and region-specific variants. This work provides a framework to understand the genetic architecture of the adaptation of wheat to diverse agricultural production environments, as well as guidelines for optimizing breeding strategies to design better wheat varieties.

The role of 14-3-3 proteins in plant growth and response to abiotic stress.

The 14-3-3 proteins widely exist in almost all plant species. They specifically recognize and interact with phosphorylated target proteins, including protein kinases, phosphatases, transcription factors and functional proteins, offering an array of opportunities for 14-3-3s to participate in the signal transduction processes. 14-3-3s are multigene families and can form homo- and heterodimers, which confer functional specificity of 14-3-3 proteins. They are widely involved in regulating biochemical and cellular processes and plant growth and development, including cell elongation and division, seed germination, vegetative and reproductive growth, and seed dormancy. They mediate plant response to environmental stresses such as salt, alkaline, osmotic, drought, cold and other abiotic stresses, partially via hormone-related signalling pathways. Although many studies have reviewed the function of 14-3-3 proteins, recent research on plant 14-3-3s has achieved significant advances. Here, we provide a comprehensive overview of the fundamental properties of 14-3-3 proteins and systematically summarize and dissect the emerging advances in understanding the roles of 14-3-3s in plant growth and development and abiotic stress responses. Some ambiguous questions about the roles of 14-3-3s under environmental stresses are reviewed. Interesting questions related to plant 14-3-3 functions that remain to be elucidated are also discussed.

Genetic relationships and identification of core germplasm among rice photoperiod- and thermo-sensitive genic male sterile lines.

BACKGROUND: Harnessing heterosis is one of the major approaches to increase rice yield and has made a great contribution to food security. The identification and selection of outstanding parental genotypes especially among male sterile lines is a key step for exploiting heterosis. Two-line hybrid system is based on the discovery and application of photoperiod- and thermo-sensitive genic sensitive male sterile (PTGMS) materials. The development of wide-range of male sterile lines from a common gene pool leads to a narrower genetic diversity, which is vulnerable to biotic and abiotic stress. Hence, it is valuable to ascertain the genetic background of PTGMS lines and to understand their relationships in order to select and design a future breeding strategy. RESULTS: A collection of 118 male sterile rice lines and 13 conventional breeding lines from the major rice growing regions of China was evaluated and screened against the photosensitive (pms3) and temperature sensitive male sterility (tms5) genes. The total gene pool was divided into four major populations as P1 possessing the pms3, P2 possessing tms5, P3 possessing both pms3 and tms5 genes, and P4 containing conventional breeding lines without any male sterility allele. The high genetic purity was revealed by homozygous alleles in all populations. The population admixture, principle components and the phylogenetic analysis revealed the close relations of P2 and P3 with P4. The population differentiation analysis showed that P1 has the highest differentiation coefficient. The lines from P1 were observed as the ancestors of other three populations in a phylogenetic tree, while the lines in P2 and P3 showed a close genetic relation with conventional lines. A core collection of top 10% lines with maximum within and among populations genetic diversity was constructed for future research and breeding efforts. CONCLUSION: The low genetic diversity and close genetic relationship among PTGMS lines in P2, P3 and P4 populations suggest a selection sweep and they might result from a backcrossing with common ancestors including the pure lines of P1. The core collection from PTGMS panel updated with new diverse germplasm will serve best for further two-line hybrid breeding.

Genome-wide association mapping for resistance to bacterial blight and bacterial leaf streak in rice.

MAIN CONCLUSION: Using genome-wide SNP association mapping, a total of 77 and 7 loci were identified for rice bacterial blight and bacterial leaf streak resistance, respectively, which may facilitate rice resistance improvement. Bacterial blight (BB) and bacterial leaf streak (BLS) caused by Gram-negative bacteria Xanthomonas oryzae pv. oryzae (Xoo) and X. oryzae pv. oryzicola (Xoc), respectively, are two economically important diseases negatively affecting rice production. To mine new sources of resistance, a set of rice germplasm collection consisting of 895 re-sequenced accessions from the 3000 Rice Genomes Project (3 K RGP) were screened for BB and BLS resistance under field conditions. Higher levels of BB resistance were observed in aus/boro subgroup, whereas the japonica, temperate japonica and tropical japonica subgroups possessed comparatively high levels of resistance to BLS. A genome-wide association study (GWAS) mined 77 genomic loci significantly associated with BB and 7 with BLS resistance. The phenotypic variance (R2) explained by these loci ranged from 0.4 to 30.2%. Among the loci, 7 for BB resistance were co-localized with known BB resistance genes and one for BLS resistance overlapped with a previously reported BLS resistance QTL. A search for the candidates in other novel loci revealed several defense-related genes that may be involved in resistance to BB and BLS. High levels of phenotypic resistance to BB or BLS could be attributed to the accumulation of the resistance (R) alleles at the associated loci, indicating their potential value in rice resistance breeding via gene pyramiding. The GWAS analysis validated the known genes underlying BB and BLS resistance and identified novel loci that could enrich the current resistance gene pool. The resources with strong resistance and significant SNPs identified in this study are potentially useful in breeding for BB and BLS resistance.

Coordination of light, circadian clock with temperature: The potential mechanisms regulating chilling tolerance in rice.

Rice (Oryza sativa L.) is a major staple food crop for over half of the world's population. As a crop species originated from the subtropics, rice production is hampered by chilling stress. The genetic mechanisms of rice responses to chilling stress have attracted much attention, focusing on chilling-related gene mining and functional analyses. Plants have evolved sophisticated regulatory systems to respond to chilling stress in coordination with light signaling pathway and internal circadian clock. However, in rice, information about light-signaling pathways and circadian clock regulation and their roles in chilling tolerance remains elusive. Further investigation into the regulatory network of chilling tolerance in rice is needed, as knowledge of the interaction between temperature, light, and circadian clock dynamics is limited. Here, based on phenotypic analysis of transgenic and mutant rice lines, we delineate the relevant genes with important regulatory roles in chilling tolerance. In addition, we discuss the potential coordination mechanism among temperature, light, and circadian clock in regulating chilling response and tolerance of rice, and provide perspectives for the ongoing chilling signaling network research in rice.

Population structure of Miscanthus sacchariflorus reveals two major polyploidization events, tetraploid-mediated unidirectional introgression from diploid M. sinensis, and diversity centred around the Yellow Sea.

BACKGROUND AND AIMS: Miscanthus, a C4 perennial grass native to East Asia, is a promising biomass crop. Miscanthus sacchariflorus has a broad geographic range, is used to produce paper in China and is one of the parents (along with Miscanthus sinensis) of the important biomass species Miscanthus × giganteus. The largest study of M. sacchariflorus population genetics to date is reported here. METHODS: Collections included 764 individuals across East Asia. Samples were genotyped with 34 605 single nucleotide polymorphisms (SNPs) derived from restriction site-associated DNA sequencing (RAD-seq) and ten plastid microsatellites, and were subjected to ploidy analysis by flow cytometry. KEY RESULTS: Six major genetic groups within M. sacchariflorus were identified using SNP data: three diploid groups, comprising Yangtze (M. sacchariflorus ssp. lutarioriparius), N China and Korea/NE China/Russia; and three tetraploid groups, comprising N China/Korea/Russia, S Japan and N Japan. Miscanthus sacchariflorus ssp. lutarioriparius was derived from the N China group, with a substantial bottleneck. Japanese and mainland tetraploids originated from independent polyploidization events. Hybrids between diploid M. sacchariflorus and M. sinensis were identified in Korea, but without introgression into either parent species. In contrast, tetraploid M. sacchariflorus in southern Japan and Korea exhibited substantial hybridization and introgression with local diploid M. sinensis. CONCLUSIONS: Genetic data indicated that the land now under the Yellow Sea was a centre of diversity for M. sacchariflorus during the last glacial maximum, followed by a series of migrations as the climate became warmer and wetter. Overall, M. sacchariflorus has greater genetic diversity than M. sinensis, suggesting that breeding and selection within M. sacchariflorus will be important for the development of improved M. × giganteus. Ornamental M. sacchariflorus genotypes in Europe and North America represent a very narrow portion of the species' genetic diversity, and thus do not well represent the species as a whole.

Allelic variation of low molecular weight glutenin subunits composition and the revealed genetic diversity in durum wheat (Triticum turgidum L. ssp. durum (Desf)).

Low molecular weight glutenin subunits (LMW-GS) play an important role in determining the bread-making characteristics of dough in the end-use quality of wheat. In this study, A total of 149 worldwide-originated durum wheat were used to analyze the composition of LMW-GS using MALDI-TOF-MS. Based on the allelic variation of glutenin subunits, the genetic diversity was evaluated for the 149 durum wheat. Five types of alleles were identified at the Glu-A3 locus with Glu-A3e, Glu-A3a/c, Glu-A3f, Glu-A3d and Glu-A3b accounting for 43.0%, 16.1%, 12.8%, 10.1% and 7.4 % of the accessions, respectively. Five types of alleles were identified at the Glu-B3 locus: Glu-B3d (60.4%), Glu-B3b (6.0%), Glu-B3c (6.0%), Glu-B3h (2.7%) and Glu-B3f (0.7%). Two novel alleles encoding abnormal subunits 40500 Da and 41260 Da were identified at the Glu-A3 and Glu-B3 loci, respectively. Further studies are needed to match these novel alleles to previously discovered novel alleles. Moreover, the genetic diversity analysis indicated that great genetic variation existed in durum wheat among encoding loci of glutenin subunits, released periods of varieties and different geographical origins. The results provide more important information of potential germplasm for the improvement of durum wheat and common wheat.

Potential unfavorable impacts of BDNF Val66Met polymorphisms on metabolic risks in average population in a longevous area.

BACKGROUND: Brain-derived neurotrophic factor (BDNF) has been implicated in cognitive performance and the modulation of several metabolic parameters in some disease models, but its potential roles in successful aging remain unclear. We herein sought to define the putative correlation between BDNF Val66Met and several metabolic risk factors including BMI, blood pressure, fasting plasma glucose (FPG) and lipid levels in a long-lived population inhabiting Hongshui River Basin in Guangxi. METHODS: BDNF Val66Met was typed by ARMS-PCR for 487 Zhuang long-lived individuals (age ≥ 90, long-lived group, LG), 593 of their offspring (age 60-77, offspring group, OG) and 582 ethnic-matched healthy controls (aged 60-75, control group, CG) from Hongshui River Basin. The correlations of genotypes with metabolic risks were then determined. RESULTS: As a result, no statistical difference was observed on the distribution of allelic and genotypic frequencies of BDNF Val66Met among the three groups (all P > 0.05) except that AA genotype was dramatically higher in females than in males of CG. The HDL-C level of A allele (GA/AA genotype) carriers was profoundly lower than was non-A (GG genotype) carriers in the total population and the CG (P = 0.009 and 0.006, respectively), which maintained in females, hyperglycemic and normolipidemic subgroup of CG after stratification by gender, BMI, glucose and lipid status. Furthermore, allele A carriers, with a higher systolic blood pressure, exhibited 1.63 folds higher risk than non-A carriers to be overweight in CG (OR = 1.63, 95% CI: 1.05 - 2.55, P = 0.012). Multiple regression analysis displayed that the TC level of LG reversely associated with BDNF Val66Met genotype. CONCLUSIONS: These data suggested that BDNF 66Met may play unfavorable roles in blood pressure and lipid profiles in the general population in Hongshui River area which might in part underscore their poorer survivorship versus the successful aging individuals and their offspring.

Enhancement of Gastric Ulcer Healing and Angiogenesis by Hepatocyte Growth Factor Gene Mediated by Attenuated Salmonella in Rats.

The present study developed an oral hepatocyte growth factor (HGF) gene therapy strategy for gastric ulcers treatment. An attenuated Salmonella typhimurium that stably expressed high HGF (named as TPH) was constructed, and the antiulcerogenic effect of TPH was evaluated in a rat model of gastric ulcers that created by acetic acid subserosal injection. From day 5 after injection, TPH (1 × 109 cfu), vehicle (TP, 1 × 109 cfu), or sodium bicarbonate (model control) was administered orally every alternate day for three times. Then ulcer size was measured at day 21 after ulcer induction. The ulcer area in TPH-treated group was 10.56 ± 3.30 mm², which was smaller when compared with those in the TP-treated and model control groups (43.47 ± 4.18 and 56.25 ± 6.38 mm², respectively). A higher level of reepithelialization was found in TPH-treated group and the crawling length of gastric epithelial cells was significantly longer than in the other two groups (P < 0.05). The microvessel density in the ulcer granulation tissues of the TPH-treated rats was 39.9 vessels/mm², which was greater than in the TP-treated and model control rats, with a significant statistical difference. These results suggest that TPH treatment significantly accelerates the healing of gastric ulcers via stimulating proliferation of gastric epithelial cells and enhancing angiogenesis on gastric ulcer site.

SNP-based association analysis for seedling traits in durum wheat (Triticum turgidum L. durum (Desf.)).

In the present study, 150 accessions of worldwide originated durum wheat germplasm (Triticum turgidum spp. durum) were observed for major seedling traits and their growth. The accessions were evaluated for major seedling traits under controlled conditions of hydroponics at the 13th, 20th, 27th and 34th day-after germination. Biomass traits were measured at the 34th day-after germination. Correlation analysis was conducted among the seedling traits and three field traits at maturity, plant height, grain weight and 1000-grain weight observed in four consecutive years. Associations of the measured seedling traits and SNP markers were analyzed based on the mixed linear model (MLM). The results indicated that highly significant genetic variation and robust heritability were found for the seedling and field mature traits. In total, 259 significant associations were detected for all the traits and four growth stages. The phenotypic variation explained (R2) by a single SNP marker is higher than 10% for most (84%) of the significant SNP markers. Forty-six SNP markers associated with multiple traits, indicating non-neglectable pleiotropy in seedling stage. The associated SNP markers could be helpful for genetic analysis of seedling traits, and marker-assisted breeding of new wheat varieties with strong seedling vigor.

Ecological characteristics and in situ genetic associations for yield-component traits of wild Miscanthus from eastern Russia.

Background and aims Miscanthus is a genus of perennial C4 grasses native to East Asia. It includes the emerging ligno-cellulosic biomass crop M. ×giganteus, a hybrid between M. sinensis and M. sacchariflorus. Biomass yield and cold tolerance are of particular interest in Miscanthus, given that this crop is more temperate adapted than its C4 relatives maize, sorghum and sugarcane. Methods A plant exploration was conducted in eastern Russia, at the northern extreme of the native range for Miscanthus, with collections including 174 clonal germplasm accessions (160 M. sacchariflorus and 14 M. sinensis) from 47 sites. Accessions were genotyped by restriction site-associated DNA sequencing (RAD-seq) and plastid microsatellites. Key Results Miscanthus sinensis was found in maritime climates near Vladivostok (43·6°N) and on southern Sakhalin Island (46·6°N). Miscanthus sacchariflorus was found inland at latitudes as high as 49·3°N, where M. sinensis was absent. Most M. sacchariflorus accessions were diploid, but approx. 2 % were tetraploids. Molecular markers revealed little population structure (Jost's D < 0·007 among diploid groups) but high genetic diversity (expected heterozygosity = 0·14) within the collection of Russian M. sacchariflorus. Genome-wide association (GWA) analysis for traits measured at the collection sites revealed three M. sacchariflorus single nucleotide polymorphisms (SNPs) significantly associated with the number of stems per unit area, one with height and one with basal stem diameter; three were near or within previously described sorghum quantitative trait loci for related traits. Conclusions This new Miscanthus germplasm collection from eastern Russia will be useful for breeding Miscanthus and sugarcane cultivars with improved adaptation to cold. Moreover, a strategy is proposed to facilitate the rapid utilization of new germplasm collections: by implementing low-cost SNP genotyping to conduct GWA studies of phenotypic data obtained at collection sites, plant breeders can be provided with actionable information on which accessions have desirable traits and alleles.

Contrasting allelic distribution of CO/Hd1 homologues in Miscanthus sinensis from the East Asian mainland and the Japanese archipelago.

The genus Miscanthus is a perennial C4 grass native to eastern Asia and is a promising candidate bioenergy crop for cool temperate areas. Flowering time is a crucial factor governing regional and seasonal adaptation; in addition, it is also a key target trait for extending the vegetative phase to improve biomass potential. Homologues of CONSTANS (CO)/Heading date 1(Hd1) were cloned from Miscanthus sinensis and named MsiHd1. Sequences of MsiHd1 homologues were compared among 24 wild M. sinensis accessions from Japan, 14 from China, and three from South Korea. Two to five MsiHd1 alleles in each accession were identified, suggesting that MsiHd1 consists of at least three loci in the Miscanthus genome. Verifying the open reading frame in MsiHd1, they were classified as putative functional alleles without mutations or non-functional alleles caused by indels. The Neighbor-Joining tree indicated that one of the multiple MsiHd1 loci is a pseudogene locus without any functional alleles. The pseudogene locus was named MsiHd1b, and the other loci were considered to be part of the MsiHd1a multi-locus family. Interestingly, in most Japanese accessions 50% or more of the MsiHd1a alleles were non-functional, whereas accessions from the East Asian mainland harboured only functional alleles. Five novel miniature inverted transposable elements (MITEs) (MsiMITE1-MsiMITE5) were observed in MsiHd1a/b. MsiMITE1, detected in exon 1 of MsiHd1a, was only observed in Japanese accessions and its revertant alleles derived from retransposition were predominantly in Chinese accessions. These differences in MsiHd1a show that the dependency on functional MsiHd1a alleles is different between accessions from the East Asian mainland and Japan.

Genetic structure of Miscanthus sinensis and Miscanthus sacchariflorus in Japan indicates a gradient of bidirectional but asymmetric introgression.

Unilateral introgression from diploids to tetraploids has been hypothesized to be an important evolutionary mechanism in plants. However, few examples have been definitively identified, perhaps because data of sufficient depth and breadth were difficult to obtain before the advent of affordable high-density genotyping. Throughout Japan, tetraploid Miscanthus sacchariflorus and diploid Miscanthus sinensis are common, and occasionally hybridize. In this study, 667 M. sinensis and 78 M. sacchariflorus genotypes from Japan were characterized using 20 704 SNPs and ten plastid microsatellites. Similarity of SNP genotypes between diploid and tetraploid M. sacchariflorus indicated that the tetraploids originated through autopolyploidy. Structure analysis indicated a gradient of introgression from diploid M. sinensis into tetraploid M. sacchariflorus throughout Japan; most tetraploids had some M. sinensis DNA. Among phenotypically M. sacchariflorus tetraploids, M. sinensis ancestry averaged 7% and ranged from 1-39%, with introgression greatest in southern Japan. Unexpectedly, rare (~1%) diploid M. sinensis individuals from northern Japan were found with 6-27% M. sacchariflorus ancestry. Population structure of M. sinensis in Japan included three groups, and was driven primarily by distance, and secondarily by geographic barriers such as mountains and straits. Miscanthus speciation is a complex and dynamic process. In contrast to limited introgression between diploid M. sacchariflorus and M. sinensis in northern China, selection for adaptation to a moderate maritime climate probably favoured cross-ploidy introgressants in southern Japan. These results will help guide the selection of Miscanthus accessions for the breeding of biomass cultivars.

PPARD +294C overrepresentation in general and long-lived population in China Bama longevity area and unique relationships between PPARD +294T/C polymorphism and serum lipid profiles.

BACKGROUND: The +294T/C polymorphism in the peroxisome proliferator-activated receptor delta (PPARD) gene is associated with hyperlipidemia in several younger populations, but results are still inconsistence across ethnic groups and its possible impact on the lipid profiles of long-lived individuals remains unexploited. Here, we aimed to evaluate the possible correlation between PPARD +294T/C and serum lipid levels in a long-lived population in Bama, a region known for longevity situated in Guangxi, China. METHODS: Genotyping of PPARD +294T/C polymorphism was conducted in 505 long-lived inhabitants (aged 90 and above, long-lived group, LG) and 468 healthy controls (aged 60-75, non-long-lived group, non-LG) recruited from Bama area. RESULTS: No difference in allelic and genotypic frequencies was found between the two groups (P>0.05). However, C-allele and C-genotype (TC and CC) were significantly more frequent in the females of non-LG than were LG after sex stratification. CC carriers exhibited higher LDL-C level in LG (P<0.05) but lower TC, TG and LDL-C in non-LG (P<0.05 for each) than TT carriers; C allele carriers (TC/CC) in LG exhibited higher TC, TG, and LDL-C levels as compared with the same genotype and the same lipid parameter in non-LG (P<0.05 for each). LDL-C in LG was correlated with genotypes while TC, TG, and LDL-C in non-LG were correlated with genotypes (P<0.05-0.001). CONCLUSION: Our results suggest that there were different impact patterns of PPARD +294T/C polymorphism on lipid profiles between long-lived cohort and average population in Bama area and this may be one of the genetic bases of its longevity.

Natural variation and genetic analysis of the tiller angle gene MsTAC1 in Miscanthus sinensis.

Biomass yield is an important target trait in Miscanthus breeding for desirable energy crops. Tiller angle is a key trait of plant architecture because it determines planting density and further influences biomass yield through affecting photosynthesis efficiency. TAC1, a major gene involved in tiller and leaf angle control in rice and maize, respectively, has been extensively studied. Nucleotide variation at this gene, MsTAC1, was investigated in 33 Miscanthus sinensis accessions collected from different areas in China, and one genotype of Miscanthus × giganteus. A total of 136 loci, including 129 single base substitutions and seven InDels, occurred within the MsTAC1 gene of 1,874 bp. The genetic diversity at MsTAC1 is characterized by high nucleotide diversity (π value) and high heterozygosity. Clustering analysis indicated that the phylogenetic tree of the 33 M. sinensis accessions was correlated with their geographical sites of origin. The neutrality test revealed no strong selection pressure on coding and non-coding region variations of the MsTAC1 gene in the accessions. Phenotype evaluations were conducted for tiller angle and five other traits in the Miscanthus panels in the first two growth years of 2009 and 2010. Analysis of variance showed significant phenotypic variations in the examined traits. Association analysis using 246 markers detected 88 loci associated with all the test traits in either 1 or 2 years, and 11 of the 88 were year reproducible and thus reliable. These associations indicate that the variation of MsTAC1 affects the phenotypic value of the tiller angle, tiller number and biomass yield, suggesting that allelic variation in MsTAC1 affects multiple traits and demonstrates its significance in Miscanthus breeding programs.

Variation in chilling tolerance for photosynthesis and leaf extension growth among genotypes related to the C4 grass Miscanthus ×giganteus.

The goal of this study was to identify cold-tolerant genotypes within two species of Miscanthus related to the exceptionally chilling-tolerant C4 biomass crop accession: M. ×giganteus 'Illinois' (Mxg) as well as in other Mxg genotypes. The ratio of leaf elongation at 10 °C/5 °C to that at 25 °C/25 °C was used to identify initially the 13 most promising Miscanthus genotypes out of 51 studied. Net leaf CO2 uptake (A sat) and the maximum operating efficiency of photosystem II (ФPSII) were measured in warm conditions (25 °C/20 °C), and then during and following a chilling treatment of 10 °C/5 °C for 11 d. Accessions of M. sacchariflorus (Msa) showed the smallest decline in leaf elongation on transfer to chilling conditions and did not differ significantly from Mxg, indicating greater chilling tolerance than diploid M. sinensis (Msi). Msa also showed the smallest reductions in A sat and ФPSII, and greater chilling-tolerant photosynthesis than Msi, and three other forms of Mxg, including new triploid accessions and a hexaploid Mxg 'Illinois'. Tetraploid Msa 'PF30153' collected in Gifu Prefecture in Honshu, Japan did not differ significantly from Mxg 'Illinois' in leaf elongation and photosynthesis at low temperature, but was significantly superior to all other forms of Mxg tested. The results suggested that the exceptional chilling tolerance of Mxg 'Illinois' cannot be explained simply by the hybrid vigour of this intraspecific allotriploid. Selection of chilling-tolerant accessions from both of Mxg's parental species, Msi and Msa, would be advisable for breeding new highly chilling-tolerant Mxg genotypes.

A footprint of past climate change on the diversity and population structure of Miscanthus sinensis.

BACKGROUND AND AIMS: Miscanthus is a perennial C4 grass that is a leading potential feedstock crop for the emerging bioenergy industry in North America, Europe and China. However, only a single, sterile genotype of M. × giganteus (M×g), a nothospecies derived from diploid M. sinensis (Msi) and tetraploid M. sacchariflorus (Msa), is currently available to farmers for biomass production. To facilitate breeding of Miscanthus, this study characterized genetic diversity and population structure of Msi in its native range of East Asia. METHODS: A total of 767 accessions were studied, including 617 Msi from most of its native range in China, Japan and South Korea, and 77 ornamental cultivars and 43 naturalized individuals from the USA. Accessions were evaluated with 21 207 restriction site-associated DNA sequencing single nucleotide polymorphism (SNP) markers, 424 GoldenGate SNPs and ten plastid microsatellite markers. KEY RESULTS: Six genetic clusters of Msi from geographically distinct regions in Asia were identified. Genetic data indicated that (1) south-eastern China was the origin of Msi populations found in temperate eastern Asia, which is consistent with this area probably having been a refugium during the last glacial maximum (LGM); (2) Msi migrated directly from south-eastern China to Japan before migrating to the same latitudes in China and Korea, which is consistent with the known sequence of warming post-LGM; (3) ornamental Msi cultivars were derived from the southern Japan population, and US naturalized populations were derived from a sub-set of the ornamental cultivars; and (4) many ornamental cultivars previously described as Msi have hybrid ancestry from Msa and Msi, whereas US naturalized populations of Msi do not. CONCLUSIONS: Population structure of Msi was driven by patterns of warming since the LGM, and secondarily by geographical barriers. This study will facilitate germplasm conservation, association analyses and identification of potential heterotic groups for the improvement of Miscanthus as a bioenergy crop.

Enrichment of MTHFR 677 T in a Chinese long-lived cohort and its association with lipid modulation.

BACKGROUND: Variants in the Methylenetetrahydrofolate reductase (MTHFR) gene may result in a lowered catalytic activity and associate with subsequent elevated serum homocysteine (Hcy) concentration, abnormal DNA synthesis and methylation, cardiovascular risk, and unhealthy aging. Several investigations on the relationship of MTHFR C677T polymorphism with serum lipid profile and longevity have been conducted in some populations, but the findings remain mixed. Herein, we sought to look at the association between MTHFR C677T and lipid profile in a longevous cohort in Bama, a well-known home of longevity in China. METHODS: Genotyping of MTHFR C677T was undertaken in 516 long-lived inhabitants (aged 90 and older, long-lived group, LG) and 493 healthy controls (aged 60-75, non-long-lived group, non-LG) recruited from Bama area. Correlation between MTHFR genotypes and lipids was then evaluated. RESULTS: T allele and TT genotype were significantly more prevalent in LG (P=0.001 and 0.002, respectively), especially in females, than in non-LG. No difference in the tested lipid measures among MTHFR C677T genotypes was observed in LG, non-LG and total population (P>0.05 for all). However, female but not male T carriers exhibited higher TC and LDL-C levels than did T noncarriers in the total population and in LG after stratification by sex (P<0.05 for each). These differences did not however remain through further subdivision by hyperlipidemia and normolipidemia. CONCLUSION: The higher prevalence of MTHFR 677 T genotypes and its modest unfavorable impact on lipids in Bama long-lived individuals may imply an existence of other protective genotypes which require further determination.

Single-cell multi-omics profiling of human preimplantation embryos identifies cytoskeletal defects during embryonic arrest.

Human in vitro fertilized embryos exhibit low developmental capabilities, and the mechanisms that underlie embryonic arrest remain unclear. Here using a single-cell multi-omics sequencing approach, we simultaneously analysed alterations in the transcriptome, chromatin accessibility and the DNA methylome in human embryonic arrest due to unexplained reasons. Arrested embryos displayed transcriptome disorders, including a distorted microtubule cytoskeleton, increased genomic instability and impaired glycolysis, which were coordinated with multiple epigenetic reprogramming defects. We identified Aurora A kinase (AURKA) repression as a cause of embryonic arrest. Mechanistically, arrested embryos induced through AURKA inhibition resembled the reprogramming abnormalities of natural embryonic arrest in terms of the transcriptome, the DNA methylome, chromatin accessibility and H3K4me3 modifications. Mitosis-independent sequential activation of the zygotic genome in arrested embryos showed that YY1 contributed to human major zygotic genome activation. Collectively, our study decodes the reprogramming abnormalities and mechanisms of human embryonic arrest and the key regulators of zygotic genome activation.

SNP-revealed genetic diversity in wild emmer wheat correlates with ecological factors.

BACKGROUND: Patterns of genetic diversity between and within natural plant populations and their driving forces are of great interest in evolutionary biology. However, few studies have been performed on the genetic structure and population divergence in wild emmer wheat using a large number of EST-related single nucleotide polymorphism (SNP) markers. RESULTS: In the present study, twenty-five natural wild emmer wheat populations representing a wide range of ecological conditions in Israel and Turkey were used. Genetic diversity and genetic structure were investigated using over 1,000 SNP markers. A moderate level of genetic diversity was detected due to the biallelic property of SNP markers. Clustering based on Bayesian model showed that grouping pattern is related to the geographical distribution of the wild emmer wheat. However, genetic differentiation between populations was not necessarily dependent on the geographical distances. A total of 33 outlier loci under positive selection were identified using a FST-outlier method. Significant correlations between loci and ecogeographical factors were observed. CONCLUSIONS: Natural selection appears to play a major role in generating adaptive structures in wild emmer wheat. SNP markers are appropriate for detecting selectively-channeled adaptive genetic diversity in natural populations of wild emmer wheat. This adaptive genetic diversity is significantly associated with ecological factors.