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Gene conversion between direct noncoding repeats promotes genetic and phenotypic diversity at a regulatory locus of Zea mays (L.).

ABSTRACT: While evolution of coding sequences has been intensively studied, diversification of noncoding regulatory regions remains poorly understood. In this study, we investigated the molecular evolution of an enhancer region located 5 kb upstream of the transcription start site of the maize pericarp color1 (p1) gene. The p1 gene encodes an R2R3 Myb-like transcription factor that regulates the flavonoid biosynthetic pathway in maize floral organs. Distinct p1 alleles exhibit organ-specific expression patterns on kernel pericarp and cob glumes. A cob glume-specific regulatory region has been identified in the distal enhancer. Further characterization of 6 single-copy p1 alleles, including P1-rr (red pericarp/red cob) and P1-rw (red pericarp and white cob), reveals 3 distinct enhancer types. Sequence variations in the enhancer are correlated with the p1 gene expression patterns in cob glume. Structural comparisons and phylogenetic analyses suggest that evolution of the enhancer region is likely driven by gene conversion between long direct noncoding repeats (approximately 6 kb in length). Given that tandem and segmental duplications are common in both animal and plant genomes, our studies suggest that recombination between noncoding duplicated sequences could play an important role in creating genetic and phenotypic variations.

SUBMITTER: Zhang F

PROVIDER: S-EPMC1602084 | biostudies-literature | 2006 Oct

REPOSITORIES: biostudies-literature

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Gene conversion between direct noncoding repeats promotes genetic and phenotypic diversity at a regulatory locus of Zea mays (L.).

Zhang Feng F Peterson Thomas T

Genetics 20060702 2

While evolution of coding sequences has been intensively studied, diversification of noncoding regulatory regions remains poorly understood. In this study, we investigated the molecular evolution of an enhancer region located 5 kb upstream of the transcription start site of the maize pericarp color1 (p1) gene. The p1 gene encodes an R2R3 Myb-like transcription factor that regulates the flavonoid biosynthetic pathway in maize floral organs. Distinct p1 alleles exhibit organ-specific expression pa ...[more]

PMID: 16816430

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Project description:The evolution of maize (Zea mays L.) is highly controversial given the discrepancies related to the phenotypic and genetic changes suffered by the species, the incidence of human groups and the times in which these changes occurred. Also, morphological and genetic traits of crops are difficult to evaluate in the absence of fossils macro-botanical remains. In contrast in the Tarapacá region (18-21° S), Atacama Desert of Chile, prehispanic settlements (ca. 2500-400 yr BP) displayed extensive maize agriculture. The presence of archaeological macro-botanical remains of maize provided a unique opportunity to study the evolution of this crop, covering a temporal sequence of at least 2000 years. Thus, in this study, we ask how the morphological and genetic diversity of maize has varied since its introduction during prehispanic times in the Tarapacá region. To answer this, we measured and compared morphological traits of size and shape between archaeological cobs and kernels and 95 ears from landraces. To established genetic diversity eight microsatellite markers (SSR) were analyzed in archaeological and modern kernels. Genetic diversity was estimated by allelic frequency rates, the average number of alleles per locus, observed heterozygosity (Ho) and expected heterozygosity (He). Differences between populations and genetic structure were estimated by fixation index FST and STRUCTURE analysis. Our results indicate significant phenotypic differences and genetic distance between archaeological maize and landraces. This result is suggestive of an introduction of new varieties or drastic selective changes in modern times in Tarapacá. Additionally, archaeological maize shows a low genetic diversity and a progressive increase in the size of ears and kernels. These results suggest a human selection during prehispanic times and establish that prehispanic farmers played an important role in maize development. They also provide new clues for understanding the evolutionary history of maize in hyperarid conditions.

Project description:Plant growth-limiting factors, such as low nutrient availability and weak pathogen resistance, may hinder the production of several crops. Plant growth-promoting bacteria (PGPB) used in agriculture, which stimulate plant growth and development, can serve as a potential tool to mitigate or even circumvent these limitations. The present study evaluated the feasibility of using bacteria isolated from the maize rhizosphere as PGPB for the cultivation of this crop. A total of 282 isolates were collected and clustered into 57 groups based on their genetic similarity using BOX-PCR. A representative isolate from each group was selected and identified at the genus level with 16S rRNA sequencing. The identified genera included Bacillus (61.5% of the isolates), Lysinibacillus (30.52%), Pseudomonas (3.15%), Stenotrophomonas (2.91%), Paenibacillus (1.22%), Enterobacter (0.25%), Rhizobium (0.25%), and Atlantibacter (0.25%). Eleven isolates with the highest performance were selected for analyzing the possible pathways underlying plant growth promotion using biochemical and molecular techniques. Of the selected isolates, 90.9% were positive for indolepyruvate/phenylpyruvate decarboxylase, 54.4% for pyrroloquinoline quinine synthase, 36.4% for nitrogenase reductase, and 27.3% for nitrite reductase. Based on biochemical characterization, 9.1% isolates could fix nitrogen, 36.6% could solubilize phosphate, 54.5% could produce siderophores, and 90.9% could produce indole acetic acid. Enzymatic profiling revealed that the isolates could degrade starch (90.1%), cellulose (72.7%), pectin (81.8%), protein (90.9%), chitin (18.2%), urea (54.5%), and esters (45.4%). Based on the data obtained, we identified three Bacillus spp. (LGMB12, LGMB273, and LGMB426), one Stenotrophomonas sp. (LGMB417), and one Pseudomonas sp. (LGMB456) with the potential to serve as PGPB for maize. Further research is warranted to evaluate the biotechnological potential of these isolates as biofertilizers under field conditions.

Dataset Information

Gene conversion between direct noncoding repeats promotes genetic and phenotypic diversity at a regulatory locus of Zea mays (L.).

Publications

Gene conversion between direct noncoding repeats promotes genetic and phenotypic diversity at a regulatory locus of Zea mays (L.).

Similar Datasets

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