Genetic Diversity of Rice Landraces from Lowland and Upland Accessions of China

Genetic diversity of rice landraces from lowland and upland accessions of China was investigated using 66 polymorphic simple sequence repeat （SSR） markers. The total number of alleles detected from all 324 tested accessions was 555 with an average allele number （Na） of 8.409 per locus, the average effective number of alleles （Ne） of 3.574 and the average Shannon＇s information index （I） of 1.378. The genetic diversity was higher for the indica landraces compared to the japonica landraces, and the upland landraces were more genetically diverse than the lowland landraces. The SSR markers, RM72, RM232, RM219, RM241, RM224 and RM3 showed the highest rates of polymorphism and these SSR markers were suitable to assess the genetic diversity of rice germplasm resources. A dendrogram of 324 accessions of lowland and upland landraces showed that all rice accessions were mainly subdivided into two groups, japonica and indica, with some being intermediate. The distribution of lowland and upland landraces among the japonica and indica rice groups was distinct, with obvious differentiation between the lowland and upland landraces in japonica rice, but no such clear distinction in indica rice.

Analysis of Genetic Similarity for Improved Japonica Rice Varieties from Different Provinces and Cities in China

To provide a genetic basis for japonica rice breeding, the genetic similarity and cluster of 139 accessions of improved japonica rice varieties from 12 provinces and cities of China were analyzed using 34 SSR markers. Totally 198 alleles were detected among these improved japonica rice varieties with the average number of alleles per pair of primers was 5.3235. RM320, RM531, RM1, RM286, and RM336 showed more alleles, which were 15, 12, 11, 9, and 9, respectively. RM320, RM336, RM286 and RM531 showed higher genetic diversity indexes; which were 2.3324, 2.0292, 1.8996, and 1.7820, respectively. The range of genetic similar index among improved japonica rice varieties from different provinces was from 0.321 to 0.914, with the average of 0.686. There was a high genetic similarity among improved japonica rice varieties from Heilongjiang, Jilin, Liaoning, Ningxia, and Yunnan, which were located in similar latitude or similar ecological environment, while there was a low genetic similarity between improved japonica rice varieties from Guizhou and Jiangsu, and other provinces which were located in more different latitudes and ecological environments. The markers of RM320, RM531, RM1, RM286, and RM336 fit to be used in analysis of genetic diversity for improved japonica rice variety. The genetic similarity among improved japonica rice varieties from different provinces was closely associated with genetic basis of parents, and was also correlated with latitude and ecological environment where the varieties were bred.

A single nucleotide substitution in the MATE transporter gene regulates plastochron and the many noded dwarf phenotype in barley(Hordeum vulgare L.)

In higher plants,the shoot apical meristem produces lateral organs in a regular spacing(phyllotaxy)and timing(plastochron).The molecular analysis of mutants associated with phyllotaxy and plastochron would increase our understanding of the mechanism of shoot architecture formation.In this study,we identified mutant mnd8ynp5 that shows an increased rate of leaf emergence and a larger number of nodes in combination with a dwarfed growth habit from an EMS-treated population of the elite barley cultivar Yangnongpi 5.Using a map-based cloning strategy,the mnd8 gene was narrowed down to a 6.7-kb genomic interval on the long arm of chromosome 5H.Sequence analysis revealed that a C to T single-nucleotide mutation occurred at the first exon(position 953)of HORVU5Hr1G118820,leading to an alanine(Ala)to valine(Val)substitution at the 318th amino acid site.Next,HORVU5Hr1G118820 was defined as the candidate gene of MND8 encoding 514 amino acids and containing two multidrug and toxic compound extrusion(MATE)domains.It is highly homologous to maize Bige1and has a conserved function in the regulation of plant development by controlling the leaf initiation rate.Examination of modern barely varieties showed that Hap-1 was the dominant haplotype and was selected in barley breeding around the world.Collectively,our results indicated that mnd8ynp5 is a novel allele of the HORVU5Hr1G118820 gene that is possibly responsible for the shortened plastochron and many noded dwarf phenotype in barley.

Identification of SNPs in barley(Hordeum vulgare L.)by deep sequencing of six reduced representation libraries

High-density genetic markers are required for genotyping and linkage mapping in identifying genes from crops with complex genomes, such as barley. As the most common variation, single nucleotide polymorphisms(SNPs) are suitable for accurate genotyping by using the next-generation sequencing(NGS) technology. Reduced representation libraries(RRLs) of five barley accessions and one mutant were sequenced using NGS technology for SNP discovery. Twenty million short reads were generated and the proportion of repetitive sequences was reduced by more than 56%. A total of 6061 SNPs were identified, and 451 were mapped to the draft sequence of the barley genome with pairing reads. Eleven SNPs were validated using length polymorphic allele-specific PCR markers.

Fast mapping of a chlorophyll b synthesis-deficiency gene in barley(Hordeum vulgare L.) via bulked-segregant analysis with reduced-representation sequencing

Bulked-segregant analysis coupled with next-generation sequencing(BSA-seq) has emerged as an efficient tool for genetic mapping of single genes or major quantitative trait loci controlling(agronomic) traits of interest. However, such a mapping-by-sequencing approach usually relies on deep sequencing and advanced statistical methods. Application of BSA-Seq based on construction of reduced-representation libraries and allele frequency analysis permitted anchoring the barley pale-green(pg) gene on chromosome 3 HL. With further marker-assisted validation, pg was mapped to a 3.9 Mb physical-map interval. In the pg mutant a complete deletion of chlorophyllide a oxygenase(HvCAO) gene was identified.Because the product of this gene converts Chl a to Chl b, the pg mutant is deficient in Chl b.An independent Chl b-less mutant line M4437_2 carried a nonsynonymous substitution(F263 L) in the C domain of HvCAO. The study demonstrates an optimized pooling strategy for fast mapping of agronomically important genes using a segregating population.

Mapping of the heading date gene HdAey2280 in Aegilops tauschii

An optimum heading date is essential for sustainable crop productivity and ensuring high yields. In the present study, F2：3 populations were generated by crossing an early-heading accession, Y2280, with a late-heading accession, Y2282. The heading dates of the F2 and F3 populations were investigated in a field study. Using publicly available simple sequence repeat （SSR） markers, the early heading date gene HdAey2280 was mapped onto Aegilops tauschfi chromosome 7DS between the flanking markers wmc438 and barc126 at distances of 15 and 9.1 cM, respectively. Further analysis indicated that HdAey2280 is a novel heading date gene. New SSR markers were developed based on the Ae. tauschfi draft genome sequence, resulting in four new markers that were linked to the heading date gene HdAey2280. The closest distance of these markers was 1.9 cM away from the gene. The results collected in this study will serve as a framework for map-based cloning and marker-assisted selection in wheat breeding programs in the future.

Shining in the dark:the big world of small peptides in plants

Small peptides represent a subset of dark matter in plant proteomes.Through differential expression patterns and modes of action,small peptides act as important regulators of plant growth and development.Over the past 20 years,many small peptides have been identified due to technical advances in genome sequencing,bioinformatics,and chemical biology.In this article,we summarize the classifi-cation of plant small peptides and experimental strategies used to identify them as well as their potential use in agronomic breeding.We review the biological functions and molecular mechanisms of small peptides in plants,discuss current problems in small peptide research and highlight future research directions in this field.Our review provides crucial insight into small peptides in plants and will contribute to a better understanding of their potential roles in biotechnology and agriculture.

The wheat MYB-related transcription factor TaMYB72 promotes flowering in rice

Through large-scale transformation analyses, Ta MYB72 was identified as a flowering time regulator in wheat. Ta MYB72 is a MYB family transcription factor localized to the nucleus. Three Ta MYB72 homologs,Ta MYB72-A, Ta MYB72-B and Ta MYB72-D, cloned from hexaploid wheat were mapped to the short arm of the group 6 chromosomes. Under the long-day conditions,over-expression of the Ta MYB72 in rice shortened the flowering time by approximately 12 d. Expression analyses suggest that Ta MYB72 may function through upregulation of florigen genes Hd3 a and RFT1.