bims-plasge 2018-11-04 papers

on Plastid genes

Issue of 2018‒11‒04
two papers selected by
Vera S. Bogdanova
Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences

Identification of novel C-repeat binding factor (CBF) genes in rye (Secale cereale L.) and expression studies.
Genetic Diversity, Population Structure, and Linkage Disequilibrium in a Spanish Common Bean Diversity Panel Revealed through Genotyping-by-Sequencing.

Gene. 2018 Oct 22. pii: S0378-1119(18)31094-1. [Epub ahead of print]684 82-94

Identification of novel C-repeat binding factor (CBF) genes in rye (Secale cereale L.) and expression studies.

Woo Joo Jung, Yong Weon Seo.

  Although rye is one of the most cold-tolerant species among temperate cereals, its huge and complex genome has prevented us from identifying agronomically useful genes. However, advances in high-throughput sequencing technology are making it increasingly possible to investigate its genome. The C-repeat binding factor (CBF) gene family controls cold tolerance in plants and its members are well conserved among eudicots and monocots, among which there are diverse homologs. Despite its large genome, only a small number of CBF genes have been identified in rye. In this study, we explored high-throughput sequencing data of the rye genome and identified 12 novel CBF genes. Sequence analyses revealed that these genes contain signature sequences of the CBF family. Chromosomal localization of the genes by PCR using wheat-rye addition lines showed that most of these are located on the long arm of chromosome 5, but also on the long arm of chromosomes 2 and 6. On the basis of comparative analyses of CBF family members in the Triticeae, CBF proteins were divided into several groups according to phylogenetic relationship and conserved motifs. Light is essential to fully induce CBF gene expression and there is specificity in the response to different types of abiotic stresses in ScCBF genes. The results of our study will assist investigations of CBF genes in the Triticeae and the mechanism of cold tolerance through the CBF-dependent pathway in plants.

Keywords:  C-repeat binding factor; Cold tolerance; Rye; Triticeae

DOI:  https://doi.org/10.1016/j.gene.2018.10.055
Genes (Basel). 2018 Oct 23. pii: E518. [Epub ahead of print]9(11):

Genetic Diversity, Population Structure, and Linkage Disequilibrium in a Spanish Common Bean Diversity Panel Revealed through Genotyping-by-Sequencing.

Ana Campa, Ester Murube, Juan José Ferreira.

  A common bean (Phaseolus vulgaris) diversity panel of 308 lines was established from local Spanish germplasm, as well as old and elite cultivars mainly used for snap consumption. Most of the landraces included derived from the Spanish common bean core collection, so this panel can be considered to be representative of the Spanish diversity for this species. The panel was characterized by 3099 single-nucleotide polymorphism markers obtained through genotyping-by-sequencing, which revealed a wide genetic diversity and a low level of redundant material within the panel. Structure, cluster, and principal component analyses revealed the presence of two main subpopulations corresponding to the two main gene pools identified in common bean, the Andean and Mesoamerican pools, although most lines (70%) were associated with the Andean gene pool. Lines showing recombination between the two gene pools were also observed, most of them showing useful for snap bean consumption, which suggests that both gene pools were probably used in the breeding of snap bean cultivars. The usefulness of this panel for genome-wide association studies was tested by conducting association mapping for determinacy. Significant marker⁻trait associations were found on chromosome Pv01, involving the gene Phvul.001G189200, which was identified as a candidate gene for determinacy in the common bean.

Keywords:  GBS; Phaseolus vulgaris; association mapping; common bean; diversity panel

DOI:  https://doi.org/10.3390/genes9110518