In silico comparison of genomic regions containing genes coding for enzymes and transcription factors for the phenylpropanoid pathway in Phaseolus vulgaris L. and Glycine max L. Merr

Abstract

Legumes contain a variety of phytochemicals derived from the phenylpropanoid pathway that have important effects on human health as well as seed coat color, plant disease resistance and nodulation. However, the information about the genes involved in this important pathway is fragmentary in common bean (Phaseolus vulgaris L.). The objectives of this research were to isolate genes that function in and control the phenylpropanoid pathway in common bean, determine their genomic locations in silico in common bean and soybean, and analyze sequences of the 4CL gene family in two common bean genotypes. Sequences of phenylpropanoid pathway genes available for common bean or other plant species were aligned, and the conserved regions were used to design sequence-specific primers. The PCR products were cloned and sequenced and the gene sequences along with common bean gene-based (g) markers were BLASTed against the Glycine max v.1.0 genome and the P. vulgaris v.1.0 (Andean) early release genome. In addition, gene sequences were BLASTed against the OAC Rex (Mesoamerican) genome sequence assembly. In total, fragments of 46 structural and regulatory phenylpropanoid pathway genes were characterized in this way and placed in silico on common bean and soybean sequence maps. The maps contain over 250 common bean g and SSR (simple sequence repeat) markers and identify the positions of more than 60 additional phenylpropanoid pathway gene sequences, plus the putative locations of seed coat color genes. The majority of cloned phenylpropanoid pathway gene sequences were mapped to one location in the common bean genome but had two positions in soybean. The comparison of the genomic maps confirmed previous studies, which show that common bean and soybean share genomic regions, including those containing phenylpropanoid pathway gene sequences, with conserved synteny. Indels identified in the comparison of Andean and Mesoamerican common bean 4CL gene sequences might be used to develop inter-pool phenylpropanoid pathway gene-based markers. We anticipate that the information obtained by this study will simplify and accelerate selections of common bean with specific phenylpropanoid pathway alleles to increase the contents of beneficial phenylpropanoids in common bean and other legumes.

Genome-wide identification and comparison of legume MLO gene family

“…The MLO distribution supported the high level of micro- and macro-synteny that exist between legume genomes 38 39 . It also further illustrated the assumption that most legume genes are likely located in syntenic regions 40 as previously demonstrated for most phenylpropanoid genes of soybean and common bean 41 . This distribution also suggested that they mainly arose from segmental duplication as it was already assumed for rice and several Rosaceae species 17 42 .…”

Mapping Snap Bean Pod and Color Traits, in a Dry Bean × Snap Bean Recombinant Inbred Population

“…The physical location of P based on our map is between the SNPs ss715649622 and ss715649327, which are at 11,251,772 and 11,388,741 base pairs (bp), respectively (see Song et al, 2015 supplemental files for physical location of SNPs). This falls within the rather broad range of 3.5 to 31.1 Mb identified by Reinprecht et al, (2013) for the location of P. Moghaddam et al, (2014) recently suggested that the underlying sequence for P consists of two gene models (Phvul.007G171300 and Phvul.007G171400) corresponding to an A. thaliana basic helix-loop-helix sequence and encompassing a region from 40,383,553 to 40,397,270 bp. The %28 Mb difference in location corresponds to %17 cM in our map.…”

Genetic Variation of Landraces of Common Bean Varying for Seed Coat Glossiness and Disease Resistance: Valuable Resources for Conservation and Breeding

“…shown that J is linked to a region containing MYB123 [26], similar to TT2 in Arabidopsis thaliana (AT5G35550.1) [27] and Glycine max [26], which acts as a key determinant in the proanthocyanidin accumulation of a developing seed [27].…”