Characterization, genetic diversity, phylogenetic relationships, and expression of the aluminum tolerance MATE1 gene in Secale species

Santos, E.; Benito, C.; Silva‐Navas, Javier; Gallego, Francisco Javier; Figueiras, A. M.; Pinto-Carnide, Olinda; Matos, Manuela

doi:10.1007/s10535-017-0749-0

Cited by 14 publications

(10 citation statements)

References 49 publications

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“…50% of the arable land on Earth [ 43 ]. Rye is one of the most Al-tolerant cereals, with the degree of tolerance depending on the allelic variant of MATE1 [ 44 ]. TLPs (taumatin-like proteins) are a family of pathogenesis-related (PR) proteins, involved in fungal pathogen response in many plant species [ 45 ].…”

Section: Introductionmentioning

confidence: 99%

Deep sampling and pooled amplicon sequencing reveals hidden genic variation in heterogeneous rye accessions

et al. 2020

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Background Loss of genetic variation negatively impacts breeding efforts and food security. Genebanks house over 7 million accessions representing vast allelic diversity that is a resource for sustainable breeding. Discovery of DNA variations is an important step in the efficient use of these resources. While technologies have improved and costs dropped, it remains impractical to consider resequencing millions of accessions. Candidate genes are known for most agronomic traits, providing a list of high priority targets. Heterogeneity in seed stocks means that multiple samples from an accession need to be evaluated to recover available alleles. To address this we developed a pooled amplicon sequencing approach and applied it to the out-crossing cereal rye (Secale cereale L.). Results Using the amplicon sequencing approach 95 rye accessions of different improvement status and worldwide origin, each represented by a pooled sample comprising DNA of 96 individual plants, were evaluated for sequence variation in six candidate genes with significant functions on biotic and abiotic stress resistance, and seed quality. Seventy-four predicted deleterious variants were identified using multiple algorithms. Rare variants were recovered including those found only in a low percentage of seed. Conclusions We conclude that this approach provides a rapid and flexible method for evaluating stock heterogeneity, probing allele diversity, and recovering previously hidden variation. A large extent of within-population heterogeneity revealed in the study provides an important point for consideration during rye germplasm conservation and utilization efforts.

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Section: Introductionmentioning

confidence: 99%

Deep sampling and pooled amplicon sequencing reveals hidden genic variation in heterogeneous rye accessions

et al. 2020

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“…Although, cultivated varieties of cereal rye has been experiencing extensive genetic bottleneck [ 23 ] due to strong selection pressure, like many other cereal crops, significant proportion of genetic diversity is maintained in landraces [ 24 , 25 ] and wild and weedy forms [ 26 , 27 ]. Furthermore, these populations contain potentially useful traits such as resistance to diseases, adaptability to biotic and abiotic stress [ 28 , 29 ]. Therefore, considering that the wild and weedy forms may crossbreed with cultivated rye [ 30 ], these taxa, along with the landraces, constitute gene pools for desirable genes, and can be regarded as genetic resource reservoirs for new niches and future breeding programs of wheat, triticale and other crops [ 22 ].…”

Section: Introductionmentioning

confidence: 99%

Phylogeny and genetic structure in the genus Secale

2018

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Secale L. is a small but important genus that includes cultivated rye. Although genetic diversity of cultivated rye is high, patterns of genetic diversity in the whole genus, and potential factors affecting the distribution of genetic diversity remain elusive. The population structure and distribution of genetic variation within Secale, and its correlation with taxonomic delimitation, cultivation status or spatial distribution in relation to geography and climate zones were analyzed in this study. A collection of 726 individual plants derived from 139 different accessions representing Secale cereale, S. vavilovii, S. strictum, and S. sylvestre were investigated using SSR analysis and sequence diversity analysis of a nuclear EST region. Our results indicated that perennial S. strictum subspecies are genetically divergent from annual forms of the genus. Existence of two distinct clusters within the annual taxa was observed, one corresponding to samples from Asia, and a second to those outside of Asia. No clear genetic structure was observed between different annual species/subspecies, indicating introgression between these taxa. The analysis of cultivated rye revealed that landrace populations from the Middle East have the highest genetic diversity, supporting the idea of the area being the center of origin for cultivated rye. Considering high adaptive potential of those populations, Middle Eastern landraces should be regarded as genetic resources reservoirs for new niches and future breeding programs.

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“…Genetic diversity studies ( Supplementary Tables 1 , 2 ) in the Secale genus are essential to better characterize its genome for breeding purposes and even within S. cereale . This genus is one of the most tolerant to Al stress ( Santos et al, 2018 ). All the estimated diversity parameters, including nucleotide diversity, were always higher between Poaceae species than between S. cereale .…”

Section: Discussionmentioning

confidence: 99%

Repression of Mitochondrial Citrate Synthase Genes by Aluminum Stress in Roots of Secale cereale and Brachypodium distachyon

et al. 2022

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Aluminum (Al) toxicity in acid soils influences plant development and yield. Almost 50% of arable land is acidic. Plants have evolved a variety of tolerance mechanisms for Al. In response to the presence of Al, various species exudate citrate from their roots. Rye (Secale cereale L.) secretes both citrate and malate, making it one of the most Al-tolerant cereal crops. However, no research has been done on the role of the mitochondrial citrate synthase (mCS) gene in Al-induced stress in the rye. We have isolated an mCS gene, encoding a mitochondrial CS isozyme, in two S. cereale cultivars (Al-tolerant cv. Ailés and Al-sensitive inbred rye line Riodeva; ScCS4 gene) and in two Brachypodium distachyon lines (Al-tolerant ABR8 line and Al-sensitive ABR1 line; BdCS4 gene). Both mCS4 genes have 19 exons and 18 introns. The ScCS4 gene was located on the 6RL rye chromosome arm. Phylogenetic studies using cDNA and protein sequences have shown that the ScCS4 gene and their ScCS protein are orthologous to mCS genes and CS proteins of different Poaceae plants. Expression studies of the ScCS4 and BdSC4 genes show that the amount of their corresponding mRNAs in the roots is higher than that in the leaves and that the amounts of mRNAs in plants treated and not treated with Al were higher in the Al-tolerant lines than that in the Al-sensitive lines of both species. In addition, the levels of ScCS4 and BdCS4 mRNAs were reduced in response to Al (repressive behavior) in the roots of the tolerant and sensitive lines of S. cereale and B. distachyon.

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Characterization, genetic diversity, phylogenetic relationships, and expression of the aluminum tolerance MATE1 gene in Secale species

Cited by 14 publications

References 49 publications

Deep sampling and pooled amplicon sequencing reveals hidden genic variation in heterogeneous rye accessions

Deep sampling and pooled amplicon sequencing reveals hidden genic variation in heterogeneous rye accessions

Phylogeny and genetic structure in the genus Secale

Repression of Mitochondrial Citrate Synthase Genes by Aluminum Stress in Roots of Secale cereale and Brachypodium distachyon

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