Abstract
BackgroundThe eukaryotic translation initiation factor 4E was shown to be involved in resistance against several potyviruses in plants, including pea. We combined our knowledge of pea germplasm diversity with that of the eIF4E gene to identify novel genetic diversity.Methodology/Principal findingsGermplasm of 2803 pea accessions was screened for eIF4E intron 3 length polymorphism, resulting in the detection of four eIF4EA-B-C-S variants, whose distribution was geographically structured. The eIF4EA variant conferring resistance to the P1 PSbMV pathotype was found in 53 accessions (1.9%), of which 15 were landraces from India, Afghanistan, Nepal, and 7 were from Ethiopia. A newly discovered variant, eIF4EB, was present in 328 accessions (11.7%) from Ethiopia (29%), Afghanistan (23%), India (20%), Israel (25%) and China (39%). The eIF4EC variant was detected in 91 accessions (3.2% of total) from India (20%), Afghanistan (33%), the Iberian Peninsula (22%) and the Balkans (9.3%). The eIF4ES variant for susceptibility predominated as the wild type. Sequencing of 73 samples, identified 34 alleles at the whole gene, 26 at cDNA and 19 protein variants, respectively. Fifteen alleles were virologically tested and 9 alleles (eIF4EA-1-2-3-4-5-6-7, eIF4EB-1, eIF4EC-2) conferred resistance to the P1 PSbMV pathotype.Conclusions/SignificanceThis work identified novel eIF4E alleles within geographically structured pea germplasm and indicated their independent evolution from the susceptible eIF4ES1 allele. Despite high variation present in wild Pisum accessions, none of them possessed resistance alleles, supporting a hypothesis of distinct mode of evolution of resistance in wild as opposed to crop species. The Highlands of Central Asia, the northern regions of the Indian subcontinent, Eastern Africa and China were identified as important centers of pea diversity that correspond with the diversity of the pathogen. The series of alleles identified in this study provides the basis to study the co-evolution of potyviruses and the pea host.
Highlights
Crop genetic diversity is an important pre-requisite for improving crop traits through breeding, since the presence of closely related and genetically uniform varieties provides an ideal genetic environment for disease epidemics to occur, as evidenced by several historical and recent events
Due to bulking of 10 plants per sample in the case of Chinese origin accessions (ATFCC), we detected high proportion (15%) of sample heterogeneity. This heterogeneity was not possible to test in USDA, IPK, Centre for Genetic Resources (CGN) and John Innes Centre (JIC) samples, as they originated from single plants, while in CzNPC and VIR samples prevailed susceptible alleles
We combined our knowledge and access to a wide range of pea germplasm [13,17] with an interest in Pea seed borne mosaic virus (PSbMV) resistance [31] and focused our analysis on the geographical distribution of selected, detectable alleles of the eIF4E gene using the polymorphism of intron 3
Summary
Crop genetic diversity is an important pre-requisite for improving crop traits through breeding, since the presence of closely related and genetically uniform varieties provides an ideal genetic environment for disease epidemics to occur, as evidenced by several historical and recent events (the 1846 potato blight in Ireland, the 1970 corn blight in the USA, or the 1999 wheat rust in Africa). The identification of specific, often rare traits requires specific screening and testing of entire, often very large collections. This is a time- and resource-intensive process. This situation improves, once a respective underlying gene is identified, especially in the case of monogenic traits. Various available genomic technologies [3,4,5,6,7] can be applied to uncover such variation Such screening of wild and cultivated germplasm for allelic variation of identified resistance genes has been receiving increased attention [2,8], as it can be efficiently substituted for phenotypic characterization. We combined our knowledge of pea germplasm diversity with that of the eIF4E gene to identify novel genetic diversity
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