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ARS Home » Midwest Area » East Lansing, Michigan » Sugarbeet and Bean Research » Research » Publications at this Location » Publication #307416
Title: Transcriptome characterization of developing bean (Phaseolus vulgaris L.) pods from two genotypes with contrasting seed zinc concentrations

Author
item ASTUDILLO, A - Michigan State University
item FERNANDEZ, A - Former ARS Employee
item Cichy, Karen

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/27/2015
Publication Date: 9/14/2015
Citation: Astudillo, A., Fernandez, A., Cichy, K.A. 2015. Transcriptome characterization of developing bean (Phaseolus vulgaris L.) pods from two genotypes with contrasting seed zinc concentrations. PLoS One. 10(9): e0137157.

Interpretive Summary: Dry beans are a staple food in many parts of the world and are a valuable source of dietary zinc and iron for people who consume largely plant based diets. Different dry bean cultivars can vary for their zinc and iron levels by two fold. Zinc and iron are often moved throughout the plant with the same or similar transporter proteins. The objective of this research was to sequence the RNA expressed in dry bean developing pods in its entirety (transcriptome) in two cultivars with different levels of seed Zn. The purpose of this work was to identify genes important for Zn and Fe movement to seeds in cultivars for which genetic variation has been characterized. This study revealed 27,198 genes expressed in the developing pods of dry bean which represents 86% of the total genes in the genome. A total of 380 genes had different expression patterns between two of the cultivars sequenced here, including three genes involved in Zn or Fe transport. This includes zinc-regulated transporter, iron regulated transporter like (ZIP), zinc-induced facilitator (ZIF) and yellow-stripe like (YSL) family genes. The identification of these differentially expressed Zn and Fe transport genes provide keys to genetic differences for seed Zn accumulation in dry bean which can be used to further increase seed Zn and Fe levels to benefit human nutrition.

Technical Abstract: Dry bean (Phaseolus vulgaris L.) seeds are a rich source of dietary zinc, especially for people consuming plant-based diets. Within P. vulgaris there is at least two-fold variation in seed Zn concentration. Genetic studies have revealed seed Zn differences to be controlled by a single gene in two closely related navy bean genotypes, Albion and Voyager. In this study, these two genotypes were grown under controlled fertilization conditions and the Zn concentration of various plant parts were determined. The two genotypes had similar levels of Zn in their leaves and pods but Voyager had 52% more Zn in its seeds than Albion. RNA was sequenced from developing pods of both genotypes. Transcriptome analysis of these genotypes identified 27,198 genes in the developing bean pods, representing 86% of the genes in the P. vulgaris genome (v 1.0 DOE-JGI and USDA-NIFA). Expression was detected in 18,438 genes. A relatively small number of genes (380) were differentially expressed between Albion and Voyager. Differentially expressed genes included three genes potentially involved in Zn transport, including zinc-regulated transporter, iron regulated transporter like (ZIP), zinc-induced facilitator (ZIF) and heavy metal associated (HMA) family genes. In addition 12,118 SNPs were identified between the two genotypes. Of the gene families related to Zn and/or Fe transport, eleven genes were found to contain SNPs between Albion and Voyager.