Genome scan of Kenyan Themeda triandra populations by AFLP markers reveals a complex genetic structure and hints for ongoing environmental selection

Dell’Acqua, Matteo; Fricano, Agostino; Gomarasca, Stefano; Caccianiga, Marco; Piffanelli, Pietro; Bocchi, Stefano; Gianfranceschi, L.

doi:10.1016/j.sajb.2014.01.013

Cited by 13 publications

(10 citation statements)

References 61 publications

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“…Canonical correspondence analysis (CCA) was done using Past software v. 2.17c ( Hammer et al 2001 ), to determine the relative importance of geographical factors in the spatial organization of genetic diversity among genotypes. This analysis, originally designed for relating species composition to different predictive variables ( Ter Braak 1986 ), has been successfully used to describe the relationship between environmental variables and genetic composition ( Angers et al 1999 ; Girard and Angers 2006 ; Dell'Acqua et al 2014 ). The analysis was performed using a geographical variables/genetic data matrix where longitude, latitude and altitude were used as geographic factors.…”

Section: Methodsmentioning

confidence: 99%

Genetic diversity and population structure of an important wild berry crop

et al. 2015

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Bilberry (Vaccinium myrtillus L.) fruits are perceived by consumers to be a health-promoting food, conferred by their high content of phenolic compounds and carotenoids. The health properties of these molecules have raised commercial interest in these berries globally, and caught the attention of breeders. Bilberry is a wild crop and represents an important source of genetic variability for blueberry breeding. Our study presents information related to the genetic diversity and structure of bilberry populations derived from Northern Europe, providing new knowledge for the development of genetic studies and for breeding purposes.

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Section: Methodsmentioning

confidence: 99%

Genetic diversity and population structure of an important wild berry crop

et al. 2015

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“…This analysis, designed to relate species composition to different predictive variables (Ter Braak 1986), has been successfully used to describe relationships between environmental or phenotypical variables and genetic composition (Angers et al 1999; Dell’Acqua et al 2014; Zoratti et al 2015). The analysis was based on a disease levels/genotype matrix.…”

Section: Methodsmentioning

confidence: 99%

Frequency of a natural truncated allele of MdMLO19 in the germplasm of Malus domestica

et al. 2017

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Podosphaera leucotricha is the causal agent of powdery mildew (PM) in apple. To reduce the amount of fungicides required to control this pathogen, the development of resistant apple cultivars should become a priority. Resistance to PM was achieved in various crops by knocking out specific members of the MLO gene family that are responsible for PM susceptibility (S-genes). In apple, the knockdown of MdMLO19 resulted in PM resistance. However, since gene silencing technologies such as RNAi are perceived unfavorably in Europe, a different approach that exploits this type of resistance is needed. This work evaluates the presence of non-functional naturally occurring alleles of MdMLO19 in apple germplasm. The screening of the re-sequencing data of 63 apple individuals led to the identification of 627 single nucleotide polymorphisms (SNPs) in five MLO genes (MdMLO5, MdMLO7, MdMLO11, MdMLO18, and MdMLO19), 127 of which were located in exons. The T-1201 insertion of a single nucleotide in MdMLO19 caused the formation of an early stop codon, resulting in a truncated protein lacking 185 amino acids, including the calmodulin-binding domain. The presence of the insertion was evaluated in 115 individuals. It was heterozygous in 64 and homozygous in 25. Twelve of the 25 individuals carrying the insertion in homozygosity were susceptible to PM. After barley, pea, cucumber, and tomato, apple would be the fifth species for which a natural non-functional mlo allele has been found.Electronic supplementary materialThe online version of this article (doi:10.1007/s11032-016-0610-8) contains supplementary material, which is available to authorized users.

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“…Recent approaches in statistics and genomics combine genotypic and bioclimatic information to identify the genomic loci responsible for environmental adaptation (Rellstab et al ., ; Rissler, ). These ‘landscape genomics’ approaches have found application in several research fields, including evolutionary studies (Sork et al ., ), screening of diversity in non‐model organisms (Dell'Acqua, et al ., ), conservation efforts (Vincent et al ., ) and epidemiology (Schwabl et al ., ). In an agronomic perspective, landscape genomics may either be applied to model species to derive detailed information on candidate genes for environmental adaptation (Dell'Acqua et al ., ; Mattila et al ., ) or used on crop landraces to identify adaptation alleles readily available for breeding (Pallotta et al ., ; Lasky et al ., ; Russell et al ., ).…”

Section: Introductionmentioning

confidence: 99%

Molecular diversity and landscape genomics of the crop wild relative Triticum urartu across the Fertile Crescent

et al. 2018

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Modern plant breeding can benefit from the allelic variation that exists in natural populations of crop wild relatives that evolved under natural selection in varying pedoclimatic conditions. In this study, next-generation sequencing was used to generate 1.3 million genome-wide single nucleotide polymorphisms (SNPs) on ex situ collections of Triticum urartu L., the wild donor of the A subgenome of modern wheat. A set of 75 511 high-quality SNPs were retained to describe 298 T. urartu accessions collected throughout the Fertile Crescent. Triticum urartu showed a complex pattern of genetic diversity, with two main genetic groups distributed sequentially from west to east. The incorporation of geographical information on sampling points showed that genetic diversity was correlated to the geographical distance (R = 0.19) separating samples from Jordan and Lebanon, from Syria and southern Turkey, and from eastern Turkey, Iran and Iraq. The wild emmer genome was used to derive the physical positions of SNPs on the seven chromosomes of the A subgenome, allowing us to describe a relatively slow decay of linkage disequilibrium in the collection. Outlier loci were described on the basis of the geographic distribution of the T. urartu accessions, identifying a hotspot of directional selection on chromosome 4A. Bioclimatic variation was derived from grid data and related to allelic variation using a genome-wide association approach, identifying several marker-environment associations (MEAs). Fifty-seven MEAs were associated with altitude and temperature measures while 358 were associated with rainfall measures. The most significant MEAs and outlier loci were used to identify genomic loci with adaptive potential (some already reported in wheat), including dormancy and frost resistance loci. We advocate the application of genomics and landscape genomics on ex situ collections of crop wild relatives to efficiently identify promising alleles and genetic materials for incorporation into modern crop breeding.

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Genome scan of Kenyan Themeda triandra populations by AFLP markers reveals a complex genetic structure and hints for ongoing environmental selection

Cited by 13 publications

References 61 publications

Genetic diversity and population structure of an important wild berry crop

Genetic diversity and population structure of an important wild berry crop

Frequency of a natural truncated allele of MdMLO19 in the germplasm of Malus domestica

Molecular diversity and landscape genomics of the crop wild relative Triticum urartu across the Fertile Crescent

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