Location: Crop Protection and Management ResearchTitle: Comparison of gene expression profiles in cultivated peanut (Arachis hypogaea) under strong artificial selection Author
Submitted to: Plant Breeding
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/15/2012
Publication Date: 10/1/2012
Citation: Chen, X., Hong, Y., Zhang, E., Liu, H., Zhou, G., Li, S., Zhu, F., Guo, B., Yu, J., Liang, X. 2012. Comparison of gene expression profiles in cultivated peanut (Arachis hypogaea) under strong artificial selection. Plant Breeding. 131:620-630. Interpretive Summary: Cultivated peanut (Arachis hypogaea L.), or groundnut, is an economically important leguminous crop widely used as a resource for edible oil and protein and as a direct source of human food around the world. Over the last half century, cultivated peanut has been subjected to intense artificial selection, resulting in dramatic changes in yield, resistance, biochemical composition and other agronomic traits. To date, however, the effects of selective breeding on genetic variation in peanut remain largely unknown. To investigate the impact of artificial selection on expression diversity, we compared gene expression profiles in pod and leaf of five widespread cultivars in Southern China through interpreting gene expression data generated using microarray technology. Gene expression in leaf showed more diversity than that in pod under our experimental conditions, indicating pod was subjected to more selection pressure in breeding programs. Pedigree selection focussing on pod for better yield resulted in low-expression polymorphisms, suggesting that nucleotide polymorphisms in regulatory elements of genes encoding controlling factors were indeed targets of breeding. Artificial selection led to low-expression polymorphisms. In pod, 3.9–23.76% of expressed genes showed variation in expression, while 10.82–26.08% of variation in gene expression was detected in leaf; nucleotide polymorphisms in regulatory elements led to low-expression polymorphisms in both tissues and cultivars, contributed to the narrow genetic diversity and might be a driving force behind the breeding of cultivated peanut.
Technical Abstract: Over the past five decades, cultivated peanut in China has been subjected to strong artificial selection in breeding programs. To investigate the impact of artificial selection on expression diversity, we compared gene expression profiles in pod and leaf of five widespread cultivars in Southern China. In terms of tissues, hierarchical clustering analysis revealed that expression data of pod and leaf generated different dendrograms owing to artificial selection. K-means analysis also showed that there were 16 gene expression patterns in leaf, while only eight in pod. In considering cultivars, a cultivar specificity index (t) was employed to characterize expression patterns, which suggested that genes having 0.15 < t < 0.85 constituted >80% of all expression patterns. Additionally, the diversity of gene expression in pod among cultivars of the ‘YY7’ pedigree decreased from 23.8% to 3.9%. Taken together, nucleotide polymorphisms in regulatory elements owing to artificial selection led to low-expression polymorphisms in both tissues and cultivars, contributed to the narrow genetic diversity and might be a driving force behind the breeding of cultivated peanut.