Identification of DELLA gene family in head cabbage and analysis of mRNA transport in the heterograft.

DELLA gene family is involved in the regulation of signal transduction of plant hormones. mRNAs of GA insensitive (GAI), the member of DELLA gene family, are also signaling molecules of long-distance transport in plants. Genome-wide identification and mRNA transport analysis of the members of DELLA gene family in head cabbage (Brassica oleracea var. capitata) can provide basic data for their application in head cabbage. In this study, five members of DELLA gene family (BoRGA1, BoRGA2, BoRGL1, BoRGL2, and BoRGL3) were identified in head cabbage using genome and transcriptome data. However, head cabbage lacked a GAI gene in its genome. The scion (head cabbage, inbred line G27) and the rootstock Chinese flowering cabbage (Brassica campestris L. ssp. chinensis var. utilis Tsen et Lee) (sijiucaixin) were cleft-grafted together to produce the heterograft. Inflorescence stem of the rootstock and the corresponding inflorescence stem in Chinese flowering cabbage seedlings (as controls) were purified and analyzed with transcriptome sequencing. The total of 8, 9, 3, 5, and 1 exogenous read(s), derived respectively from BoRGA1, BoRGA2, BoRGL1, BoRGL2, and BoRGL3, were identified in the transcriptomes of the rootstocks. Nevertheless, mRNA transport of DELLA family genes from scion to rootstock did not increase the transcriptional level of the members of DELLA gene family in the rootstocks. Correlation analysis suggested that mRNA transport efficiency of the DELLA family genes was correlated with the sequence and the transcriptional level of the respective DELLA gene in the scion (head cabbage). This study lays the foundation for further investigation on the molecular mechanism of mRNA transport of the members of DELLA gene family in head cabbage.

Soybean TCP transcription factors: Evolution, classification, protein interaction and stress and hormone responsiveness.

TEOSINTE-BRANCHED1/CYCLOIDEA/PCF (TCP) transcription factors, a family of plant-specific proteins, play crucial roles in plant growth and development and stress response. However, systematical information is unknown regarding the TCP gene family in soybean. In the present study, a total of 54 GmTCPs were identified in soybean, which were grouped into 11 groups with the typical TCP conserved domains. Phylogenetic relationship, protein motif and gene structure analyses distinguished the GmTCPs into two homology classes: Class I and Class II. Class II was then differentiated into two subclasses: CIN and CYC/TB1. Unique cis-element number and composition existed in the promoter regions which might be involved in the gene transcriptional regulation of different GmTCPs. Tissue expression analysis demonstrated the diverse spatiotemporal expression profiles of GmTCPs. Furthermore, the interaction protein of one previously functionally unknown TCP protein-GmTCP8 was investigated. Yeast two-hybrid assay showed the interaction between GmTCP8 and an abscisic acid receptor (GmPYL10). QRT-PCR assays indicated the distinct expression profiles of GmTCPs in response to abiotic stresses (heat, drought and salt) and stress-related signals (abscisic acid, brassinolide, salicylicacid and methyl jasmonate). These results will facilitate to uncover the possible roles of GmTCPs under abiotic stress and hormone signal responses in soybean.

Identification of the AQP members involved in abiotic stress responses from Arabidopsis.

Aquaporins (AQPs) constitute a highly diverse family of water channel proteins that play crucial biological functions in plant growth and development and stress physiology. In Arabidopsis, 35 AQPs are classified into four subfamilies (PIPs, TIPs, NIPs and SIPs). However, knowledge about the roles of different subfamily AQPs remains limited. Here, we explored the chromosomal location, gene structure and expression patterns of all AQPs in different tissues or under different abiotic stresses based on available microarray data. Tissue expression analysis showed that different AQPs had various expression patterns in tissues (root, leaf, flower and seed). Expression profiles under stress conditions revealed that most AQPs were responsive to osmotic, salt and drought stresses. Phenotypic and physiological identification showed that Tip2;2 loss-of-function mutant exhibited less sensitive to abiotic stresses (mannitol, NaCl and PEG) compared with wild-type, as evident by analysis of germination rate, root growth, survival rate, ion leakage, malondialdehyde (MDA) and proline contents. Mutant of TIP2;2 modulated the transcript levels of SOS1, SOS2, SOS3, DREB1A, DREB2A and P5CS1, under abiotic stress conditions. This study provides a basis for further functional identification of stress-related candidate AQPs in Arabidopsis.

Determination of the genetic diversity of vegetable soybean [Glycine max (L.) Merr.] using EST-SSR markers.

The development of expressed sequence tag-derived simple sequence repeats (EST-SSRs) provided a useful tool for investigating plant genetic diversity. In the present study, 22 polymorphic EST-SSRs from grain soybean were identified and used to assess the genetic diversity in 48 vegetable soybean accessions. Among the 22 EST-SSR loci, tri-nucleotides were the most abundant repeats, accounting for 50.00% of the total motifs. GAA was the most common motif among tri-nucleotide repeats, with a frequency of 18.18%. Polymorphic analysis identified a total of 71 alleles, with an average of 3.23 per locus. The polymorphism information content (PIC) values ranged from 0.144 to 0.630, with a mean of 0.386. Observed heterozygosity (Ho) values varied from 0.0196 to 1.0000, with an average of 0.6092, while the expected heterozygosity (He) values ranged from 0.1502 to 0.6840, with a mean value of 0.4616. Principal coordinate analysis and phylogenetic tree analysis indicated that the accessions could be assigned to different groups based to a large extent on their geographic distribution, and most accessions from China were clustered into the same groups. These results suggest that Chinese vegetable soybean accessions have a narrow genetic base. The results of this study indicate that EST-SSRs from grain soybean have high transferability to vegetable soybean, and that these new markers would be helpful in taxonomy, molecular breeding, and comparative mapping studies of vegetable soybean in the future.

Development and characterization of 41 novel EST-SSR markers for Pisum sativum (Leguminosae).

PREMISE OF THE STUDY: Expressed sequence tag (EST)-derived simple sequence repeat (SSR) markers were developed in Pisum sativum for further use in genetic studies and breeding programs. METHODS AND RESULTS: Forty-one novel EST-SSR primers were developed and characterized for size polymorphism in 32 Pisum sativum individuals from four populations from China. In each population, the number of alleles per locus ranged from one to seven, with observed heterozygosity and expected heterozygosity ranging from 0 to 0.8889 and 0 to 0.8400, respectively. Furthermore, 53.7% of these markers could be transferred to the related species, Vicia faba. CONCLUSIONS: The developed markers have potential for application in the study of genetic diversity, germplasm appraisal, and marker-assisted breeding in pea and other legume species.

Developing new SSR markers from ESTs of pea (Pisum sativum L.).

The development of expressed sequence tags (ESTs) from pea has provided a useful source for mining novel simple sequence repeat (SSR) markers. In the present research, in order to find EST-derived SSR markers, 18 552 pea ESTs from the National Center for Biotechnology Information (NCBI) database were downloaded and assembled into 10 086 unigenes. A total of 586 microsatellites in 530 unigenes were identified, indicating that merely 5.25% of sequences contained SSRs. The most abundant SSRs within pea were tri-nucleotide repeat motifs, and among all the tri-nucleotide repeats, the motif GAA was the most abundant type. In total, 49 SSRs were used for primer design. EST-SSR loci were subsequently screened on 10 widely adapted varieties in China. Of these, nine loci showed polymorphic profiles that revealed two to three alleles per locus. The polymorphism information content value ranged from 0.18 to 0.58 with an average of 0.41. Furthermore, transferable analysis revealed that some of these loci showed transferability to faba bean. Because of their polymorphism and transferability, these nine novel EST-SSRs will be valuable tools for marker-assisted breeding and comparative mapping of pea in the future.

Generation and characterization of 11 novel est derived microsatellites from Vicia faba (Fabaceae).

PREMISE OF THE STUDY: Simple sequence repeat (SSR) markers were developed for faba bean using expressed sequence tags (ESTs) from the NCBI database to study for genetic diversity. • METHODS AND RESULTS: A total of 11 novel EST-SSR loci were generated and characterized when tested on four populations of 29 faba bean individuals from China and Europe. The number of alleles (A) ranged from 1 to 3 in each population, and observed heterozygosity (H(O)) and expected heterozygosity (H(E)) ranged from 0 to 0.5000 and 0.6400, respectively. Furthermore, transferable analysis revealed that eight of these loci (72.73%) amplified in Pisum sativum L., six of which (75.00%) detected polymorphism. • CONCLUSIONS: The developed markers in this study will provide valuable tools for genetic diversity, resource conservation, genetic mapping, and marker-assisted breeding of faba bean in the future.