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Yang T.,Chinese Academy of Agricultural Sciences | Bao S.-Y.,Yunnan Academy of Agricultural Sciences | Ford R.,University of Melbourne | Jia T.-J.,Chinese Academy of Agricultural Sciences | And 7 more authors.
BMC Genomics | Year: 2012

Background: Faba bean (Vicia faba L.) is an important food legume crop, grown for human consumption globally including in China, Turkey, Egypt and Ethiopia. Although genetic gain has been made through conventional selection and breeding efforts, this could be substantially improved through the application of molecular methods. For this, a set of reliable molecular markers representative of the entire genome is required.Results: A library with 125,559 putative SSR sequences was constructed and characterized for repeat type and length from a mixed genome of 247 spring and winter sown faba bean genotypes using 454 sequencing. A suit of 28,503 primer pair sequences were designed and 150 were randomly selected for validation. Of these, 94 produced reproducible amplicons that were polymorphic among 32 faba bean genotypes selected from diverse geographical locations. The number of alleles per locus ranged from 2 to 8, the expected heterozygocities ranged from 0.0000 to 1.0000, and the observed heterozygosities ranged from 0.0908 to 0.8410. The validation by UPGMA cluster analysis of 32 genotypes based on Nei's genetic distance, showed high quality and effectiveness of those novel SSR markers developed via next generation sequencing technology.Conclusions: Large scale SSR marker development was successfully achieved using next generation sequencing of the V. faba genome. These novel markers are valuable for constructing genetic linkage maps, future QTL mapping, and marker-assisted trait selection in faba bean breeding efforts. © 2012 Yang et al.; licensee BioMed Central Ltd. Source

Wang C.-R.,Qingdao Agricultural University | Zhang X.-J.,Qingdao Agricultural University | Zhang H.-B.,Qingdao Academy of Agricultural science | Wu H.,Qingdao Agricultural University | Yang S.-L.,Qingdao Agricultural University
Modern Food Science and Technology | Year: 2013

The characteristics of vinegar fermented with twenty-five different pumpkin varieties were comprehensively compared by the methods of Correlation Analysis, Grey Relational Grade Analysis and Cluster Analysis. 21 pumpkin varieties, provided by Qingdao academy of agricultural sciences, were compared with 4 commercial-available pumpkin varieties. The results indicated that the single fruit weight of pumpkin was in positive correlations with the quality traits of fruit thickness, juice yield and reducing sugar content, but in negative correlation with total sugar content. 25 pumpkin varieties were clustered into 5 groups. In Group I, X2, X10, X16, X17, X20 and X21 were closest to the ideal characteristics of high reducing sugar, total sugar, juice yield and carotene content, which showed potential for vinegar fermentation. These results provided references for the selection and breeding of fine varieties of raw materials in pumpkin-processing industry in China. Source

Yuan Y.,Zhejiang Academy of Agricultural Sciences | Zhao M.,Qingdao Academy of Agricultural science | Zhang Z.,Zhejiang Academy of Agricultural Sciences | Chen T.,Chinese Academy of Agricultural Sciences | And 2 more authors.
Journal of Agricultural and Food Chemistry | Year: 2012

The effect of different fertilizers on the δ 15N value, nitrate concentration, and nitrate reductase activity of Brassica campestris and the δ 15N value of soil has been investigated through a pot experiment. The δ 15N mean value of B. campestris at the seedling stage observed in the composted chicken treatment (+8.65%) was higher than that of chemical fertilizer treatment (+5.73%), compost-chemical fertilizer (+7.53%), and control check treatment (+7.86%). There were significantly different δ 15N values (p < 0.05) between B. campestris cultivated with composted chicken manure treatment and with chemical fertilizer treatment. The similar results were also found at the middle stage and the terminal stage. The variation of δ 15N value in soil for different treatments was smaller than that of B. campestris, which was +6.71-+8.12%, +6.83-+8.24%, and +6.85-8.4%, respectively, at seedling stage, middle stage, and terminal stage. With the growth of B. campestris, the nitrate content decreased in all treatments, and the nitrate reductase activity in B. campestris increased except for the CK. Results suggested that the δ 15N values of B. campestris and soil were more effected by the fertilizer than by the dose level, and the δ 15N value analysis could be used as a tool to discriminate the B. campestris cultivated with composted manure or chemical fertilizer. © 2012 American Chemical Society. Source

Jiang Q.,Chinese Academy of Agricultural Sciences | Hou J.,Chinese Academy of Agricultural Sciences | Hao C.,Chinese Academy of Agricultural Sciences | Wang L.,Chinese Academy of Agricultural Sciences | And 3 more authors.
Functional and Integrative Genomics | Year: 2011

Sucrose synthase catalyzes the reaction sucrose + UDP → UDP-glucose + fructose, the first step in the conversion of sucrose to starch in endosperm. Previous studies identified two tissue-specific, yet functionally redundant, sucrose synthase (SUS) genes, Sus1 and Sus2. In the present study, the wheat Sus2 orthologous gene (TaSus2) series was isolated and mapped on chromosomes 2A, 2B, and 2D. Based on sequencing in 61 wheat accessions, three single-nucleotide polymorphisms (SNPs) were detected in TaSus2-2B. These formed two haplotypes (Hap-H and Hap-L), but no diversity was found in either TaSus2-2A or TaSus2-2D. Based on the sequences of the two haplotypes, we developed a co-dominant marker, TaSus2-2B tgw, which amplified 423 or 381-bp fragments in different wheat accessions. TaSus2-2B tgw was located between markers Xbarc102.2 and Xbarc91 on chromosome 2BS in a RIL population from Xiaoyan 54 × Jing 411. Association analysis suggested that the two haplotypes were significantly associated with 1,000 grain weight (TGW) in 89 modern wheat varieties in the Chinese mini-core collection. Mean TGW difference between the two haplotypes over three cropping seasons was 4.26 g (varying from 3.71 to 4.94 g). Comparative genomics analysis detected major kernel weight QTLs not only in the chromosome region containing TaSus2-2B tgw, but also in the collinear regions of TaSus2 on rice chromosome 7 and maize chromosome 9. The preferred Hap-H haplotype for high TGW underwent very strong positive selection in Chinese wheat breeding, but not in Europe. The geographic distribution of Hap-H was perhaps determined by both latitude and the intensity of selection in wheat breeding. © 2010 Springer-Verlag. Source

Chen J.,Chinese Academy of Agricultural Sciences | Chen J.,Nanyang Normal University | Zhang X.,Qingdao Academy of Agricultural science | Jing R.,Chinese Academy of Agricultural Sciences | And 3 more authors.
Theoretical and Applied Genetics | Year: 2010

Δ1-pyrroline-5-carboxylate synthetase (P5CS) is the rate-limiting enzyme involved in the biosynthesis of proline in plants. By the 3′ rapid amplification of cDNA ends (3′-RACE) approach, a 2,246-bp cDNA sequence was obtained from common bean (Phaseolus vulgaris L.), denominated PvP5CS2 differing from another P5CS gene that we cloned previously from common bean (PvP5CS). The predicted amino acid sequence of PvP5CS2 has an overall 93.2% identity GmP5CS (Glycine max L. P5CS). However, PvP5CS2 shows only 83.7% identity in amino acid sequence to PvP5CS, suggesting PvP5CS2 represents a homolog of the soybean P5CS gene. Abundant indel (insertion and deletion events) and SNP (single nucleotide polymorphisms) were found in the cloned PvP5CS2 genome sequence when comparing 24 cultivated and 3 wild common bean accessions and these in turn reflected aspects of common bean evolution. Sequence alignment showed that genotypes from the same gene pool had similar nucleotide variation, while genotypes from different gene pools had distinctly different nucleotide variation for PvP5CS2. Furthermore, diversity along the gene sequence was not evenly distributed, being low in the glutamic-g-semialdehyde dehydrogenase catalyzing region, moderate in the Glu-5-kinase catalyzing region and high in the intervening region. Neutrality tests showed that PvP5CS2 was a conserved gene undergoing negative selection. A new marker (Pv97) was developed for genetic mapping of PvP5CS2 based on an indel between DOR364 and G19833 sequences and the gene was located between markers Bng126 and BMd045 on chromosome b01. The relationship of PvP5CS2 and a previously cloned pyrroline-5-carboxylate synthetase gene as well as the implications of this work on selecting for drought tolerance in common bean are discussed. © 2010 Springer-Verlag. Source

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