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Zhang T.,Chinese Academy of Agricultural Sciences | Yu L.-X.,U.S. Department of Agriculture | McCord P.,U.S. Department of Agriculture | Miller D.,DuPont Pioneer | And 7 more authors.
PLoS ONE | Year: 2014

Verticillium wilt, caused by the soilborne fungus, Verticillium alfalfae, is one of the most serious diseases of alfalfa (Medicago sativa L.) worldwide. To identify loci associated with resistance to Verticillium wilt, a bulk segregant analysis was conducted in susceptible or resistant pools constructed from 13 synthetic alfalfa populations, followed by association mapping in two F1 populations consisted of 352 individuals. Simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers were used for genotyping. Phenotyping was done by manual inoculation of the pathogen to replicated cloned plants of each individual and disease severity was scored using a standard scale. Marker-trait association was analyzed by TASSEL. Seventeen SNP markers significantly associated with Verticillium wilt resistance were identified and they were located on chromosomes 1, 2, 4, 7 and 8. SNP markers identified on chromosomes 2, 4 and 7 co-locate with regions of Verticillium wilt resistance loci reported in M. truncatula. Additional markers identified on chromosomes 1 and 8 located the regions where no Verticillium resistance locus has been reported. This study highlights the value of SNP genotyping by high resolution melting to identify the disease resistance loci in tetraploid alfalfa. With further validation, the markers identified in this study could be used for improving resistance to Verticillium wilt in alfalfa breeding programs. Source

Yu L.,Central China Normal University | Ding G.,National Key Laboratory of Crop Genetic Improvement | Huai Z.,National Key Laboratory of Crop Genetic Improvement | Zhao H.,Huazhong Agricultural University | Zhao H.,National Key Laboratory of Crop Genetic Improvement
Field Crops Research | Year: 2013

Miscanthus has been rated as one of the most promising bioenergy crops due to its potential for biomass production. The sustainable production of Miscanthus for bioenergy feedstock partly depends on the varieties that are efficient in terms of nutrient use for the production of biomass. In this study, 23 Miscanthus accessions, collected from wide range of geographic regions, were established early in March 2010 in Wuhan, China. The feedstock was sampled for nutrient concentration determination late in November 2010 and 2011 (at physiological maturity), and harvested early in February 2011 and 2012 (after a killing frost) to evaluate the biomass yield, nutrient concentration and removal. Across these two years, the biomass yield was negatively related to the latitude of the original collection sites. A significant increase in biomass production was observed in the second growth year relative to that in the first growth year among almost all of the Miscanthus accessions. The accessions of MS267 and MS321 only yielded 1.32 and 1.91tonha-1 in 2010, respectively, but the biomass yield increased dramatically to 11.23 and 22.76tonha-1 in 2011, leading to greater nutrient removal by the final harvest and thus the requirement of much more fertilizer in the following years. The accessions MS92, MS145, MS262, MS436 and MS438 established poor biomass yields, averaging <1tonha-1 in the first two years, which suggests that they may be unsuitable for planting in the present environment. Significant differences between accessions were found for the nutrient concentration at maturity and after frost. Notable differences in the nutrient concentration after frost and nutrient removal were presented among the Miscanthus accessions. In addition, the significant difference conferred the possibility of achieving a desirable cultivar with significant biomass yield and relative nutrient removal by harvest. The accessions MS434, MS461 and MS296 had consistently high biomass yield and relatively low nutrient removal, demonstrating desirable characteristics as a low-input bioenergy crop. The results are important for guiding the agronomical practices of nutrient management and genetic improvement for nutrient-use efficiency to increase biomass production with low fertilizer input. © 2013 Elsevier B.V. Source

Wang B.,Henan Agricultural University | Wang B.,Henan University of Science and Technology | Xue Y.,Henan Agricultural University | Zhang Z.,National Key Laboratory of Crop Genetic Improvement | And 3 more authors.
Plant Growth Regulation | Year: 2015

To detect microRNAs (miRNAs) involved in determining kernel row number in maize, next generation deep sequencing was performed on an elite inbred line Zong3 (row number 14–16) of maize in China and a single segment substitution line (SSSL) SSL-10 (row number 8–10) derived from the same genetic background. In SSL-10, the single segment is inserted in chromosome 1 between molecular marker bnlg1953 and bnlg1811. Twenty-eight miRNAs belonging to 11 conserved miRNA families in maize showed expression differences >2-fold in the two lines, among which 14 members from four miRNA families were up-regulated and 14 members from 7 miRNA families were repressed in SSL-10. A genome wide degradome was sequenced to validate the miRNA target genes in solid experiment. In addition, novel miRNAs associated with ear development were predicted using a series of strict criteria, and 29 miRNAs representing eight families were predicted as novel miRNAs. Among the novel miRNAs, only one showed an expression difference >2-fold. The conserved and novel miRNAs with >2-fold expression differences were treated as candidate miRNAs involved in maize kernel row number determination. MiRNA-dependent gene expression regulation and physiological and morphological effects on ear development may explain why the SSSL changed kernel row number compared with its recurrent parent. Based on the interaction of miRNAs and their target genes, a possible miRNA-dependent pathway leading to the given DNA fragment inducing a change in kernel row number was proposed. © 2015 Springer Science+Business Media Dordrecht Source

Zhao H.,National Key Laboratory of Crop Genetic Improvement | Zhao H.,Huazhong Agricultural University | Huai Z.,National Key Laboratory of Crop Genetic Improvement | Xiao Y.,National Key Laboratory of Crop Genetic Improvement | And 7 more authors.
Planta | Year: 2014

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. © 2014 Springer-Verlag Berlin Heidelberg. Source

Sun W.,National Key Laboratory of Crop Genetic Improvement | Sun W.,Huazhong Agricultural University | Zhou Q.,Huazhong Agricultural University | Yao Y.,Huazhong Agricultural University | And 5 more authors.
PLoS ONE | Year: 2015

Grain chalkiness is an important grain quality related to starch granules in the endosperm. A high percentage of grain chalkiness is a major problem because it diminishes grain quality in rice. Here, we report quantitative trait loci identification for grain chalkiness using high-throughput single nucleotide polymorphism genotyping of a chromosomal segment substitution line population in which each line carried one or a few introduced japonica cultivar Nipponbare segments in the genetic background of the indica cultivar ZS97. Ten quantitative trait loci regions were commonly identified for the percentage of grain chalkiness and the degree of endosperm chalkiness. The allelic effects at nine of these quantitative trait loci reduced grain chalkiness. Furthermore, a quantitative trait locus (qPGC8-2) on chromosome 8 was validated in a chromosomal segment substitution line-derived segregation population, and had a stable effect on chalkiness in a multiple-environment evaluation of the near-isogenic lines. Residing on the qPGC8-2 region, the isoamylase gene (ISA1) was preferentially expressed in the endosperm and revealed some nucleotide polymorphisms between two varieties, Nipponbare and ZS97. Transgenic lines with suppression of ISA1 by RNA interference produced grains with 20% more chalkiness than the control. The results support that the gene may underlie qPGC8-2 for grain chalkiness. The multipleenvironment trials of the near-isogenic lines also show that combination of the favorable alleles such as the ISA1 gene for low chalkiness and the GS3 gene for long grains considerably improved grain quality of ZS97, which proves useful for grain quality improvement in rice breeding programs. © 2015 Sun et al. Source

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