Leveraging barrel medic genome sequence for the development and use of genomic resources for genetic analysis and breeding in legumes

BACKGROUND: A total of 62,591 cowpea expressed sequence tags (ESTs) were BLAST aligned to the whole-genome sequence of barrel medic (Medicago truncatula) to develop conserved intron scanning primers (CISPs). The efficacy of the primers was tested across 10 different legumes and on different varieties of cowpea, chickpea, and pigeon pea. Genetic diversity was assessed using the same primers on different cowpea genotypes. Singlenucleotide polymorphisms (SNPs) were detected, which were later converted to length polymorphism markers for easy genotyping. CISPs developed in this study were used in tagging resistance to bacterial leaf blight disease in cowpea. RESULTS: A total of 1262 CISPs were designed. The single-copy amplification success rates using these primers on 10 different legumes and on different varieties of cowpea, chickpea, and pigeon pea were approximately 60% in most of the legumes except soybean (47%) and peanut (37%). Genetic diversity analysis of 35 cowpea genotypes using 179 CISPs revealed 123 polymorphic markers with PIC values ranging from 0.05 to 0.59. Potential SNPs identified in cowpea, chickpea, and pigeon pea were converted to PCR primers of various sizes for easy genotyping. Using the markers developed in this study, a genetic linkage map was constructed with 11 linkage groups in cowpea. QTL mapping with 194 F3 progeny families derived from the cross C-152 × V-16 resulted in the identification of three QTLs for resistance to bacterial leaf blight disease. Conclusions: CISPs were proved to be efficient markers to identify various other marker classes like SNPs through comparative genomic studies in lesser studied crops and to aid in systematic sampling of the entire genome for well-distributed markers at low cost

Analysis of histone modification of MtSERK1 during in vitro regeneration in Medicago truncatula / 生物工程学报

Epigenetic modification, especially histone modification, plays an important role in maintaining plant genome stability, regulating gene expression and promoting regeneration in vitro. MtSERK1 is an important marker gene involved in establishing of embryogenic callus during in vitro regeneration of Medicago truncatula. In order to understand the regulation Epigenetic modification, especially histone modification, plays an important role in maintaining plant genome stability, regulating gene expression and promoting regeneration in vitro. MtSERK1 is an important marker gene involved in establishing of embryogenic callus during in vitro regeneration of Medicago truncatula. In order to understand the regulation relationship between dynamic histone modification and MtSERK1s expression during the processes of in vitro organogenesis, the expression of MtSERK1 was analyzed by qRT-PCR, and the modification status of H3K9me2, H3K4me3 and H3K9ac in the promoter region and different regions included in the gene body was analyzed by chromatin immunoprecipitation (ChIP). We found expression activation of MtSERK1 was related to the dynamic changes of histone H3K4me3 and H3K9ac in the 5' and 3' regions. This study will provide important theoretical guidance for understanding of the regulatory mechanism of MtSERK1 and also for establishing efficient genetic transformation system of Medicago truncatula.

La rizobacteria promotora del crecimiento vegetal Arthrobacter agilis UMCV2 coloniza endofíticamente a Medicago truncatula / The plant growth-promoting rhizobacterium Arthrobacter agilis UMCV2 endophytically colonizes Medicago truncatula

Arthrobacter agilis UMCV2 es una bacteria rizosférica que promueve el crecimiento vegetal de plantas leguminosas proveyéndoles hierro soluble. Un segundo mecanismo de promoción se da a través de la producción de compuestos volátiles que estimulan los mecanismos de absorción de hierro. Adicionalmente, A. agilis UMCV2 tiene la capacidad de inhibir el crecimiento de organismos fitopatógenos. En el presente trabajo se emplea una combinación de las técnicas de reacción en cadena de la polimerasa cuantitativa e hibridación in situ con fluorescencia para detectar y cuantificar la presencia de la bacteria en los tejidos internos de la planta leguminosa Medicago truncatula. Nuestros resultados demuestran que A. agilis UMCV2 se comporta como una bacteria endófita de M. truncatula especialmente en medios donde el hierro está disponible.

Arthrobacter agilis UMCV2 is a rhizosphere bacterium that promotes legume growth by solubilization of iron, which is supplied to the plant. A second growth promotion mechanism produces volatile compounds that stimulate iron uptake activities. Additionally, A. agilis UMCV2 is capable of inhibiting the growth of phytopathogens. A combination of quantitative polymerase chain reaction and fluorescence in situ hybridization techniques were used here to detect and quantify the presence of the bacterium in the internal tissues of the legume Medicago truncatula. Our results demonstrate that A. agilis UMCV2 behaves as an endophytic bacterium of M. truncatula, particularly in environments where iron is available.

Full-length cDNA cloning and bioinformatics analysis of PnUGT1 gene in Panax notoginseng / 药学学报

After searching the transcriptome dataset of Panax notoginseng, one unique sequence Pn02086 encoding UDP-glucosyltransferase (UGT), which may be involved in triterpene saponin biosynthesis, was discovered. The open reading frame of the UGT gene, named as PnUGT1, was cloned by 5'-RACE and RT-PCR method from P. notoginseng. The GenBank accession number for this gene is JX018210. The bioinformatic analysis of this gene and its corresponding protein was performed. The PnUGT1 gene contains a 1488 bp open reading frame and encodes a predicted protein of 495 amino acids. The molecular weight is 55.453 kD and the protein is unstable. In the secondary structure, the percentage of alpha helix, beta turn, random coil were 36.16%, 11.31%, 52.53%, respectively. The PnUGT1 contains 7 conserved domains predicted by InterProScan, including PSPG-box which is a unique consensus sequence of glycosyltransferases involved in plant secondary metabolism. The PnUGT1 was most likely to be located in the cytoplasm, without signal peptide and transmembrane region. Sequence alignment and phylogenetic analysis demonstrated that PnUGT1 had relative close relationship to the triterpene UDP-glucosyltransferase of Medicago truncatula (AAW56092), with the 66% similarity of conserved domain PSPG-box. PnUGT1 was more abundant in P. notoginseng leaf than in flower, stem and root. Therefore, PnUGT1 gene may be involved in notoginsenoside biosynthesis.