Evolution of Gene Expression Balance Among Homeologs of Natural Polyploids

Mutti, Jasdeep S.; Bhullar, Ramanjot K; Gill, Kulvinder S.

doi:10.1534/g3.116.038711

Cited by 26 publications

(24 citation statements)

References 76 publications

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“…5A-B) and subcellular localization (Table S2). SV between homeologs might result in different gene regulation of gene expression and consequently lead to novel functions 33 . Diverse gene expression patterns among FaMLO genes across different tissues (Fig.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification and Characterization of MLO Gene Family in Octoploid Strawberry (Fragaria ×ananassa)

Tapia

Barbey

Chandra

et al. 2020

Preprint

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Powdery mildew (PM) caused by Podosphaera aphanis is a major fungal disease in cultivated strawberry. Mildew Resistance Locus O (MLO) is a gene family described for having conserved seven-transmembrane domains. Induced loss-of-function in specific MLO genes can confer durable and broad resistance against PM pathogens. However, the underlying biological role of MLO genes in strawberry is still unknown. In the present study, the genomic structure of MLO genes were characterized in both diploid (Fragaria vesca) and octoploid strawberry (Fragaria ×ananassa), and the potential sources of MLO-mediated susceptibility were identified. Twenty MLO-like sequences were identified in F. vesca, with sixty-eight in F. ×ananassa. Phylogenetic analysis divides strawberry MLO genes into eight different clades, in which three FveMLO and ten FaMLO genes were grouped together with the functionally known MLO susceptibility. Out of ten FaMLO genes, FaMLO17-2 and FaMLO17-3 showed the highest similarity to the known susceptibility MLO proteins. Gene expression analysis of FaMLO genes was conducted using a multi-parental segregating population. Three expression quantitative trait loci (eQTL) were substantially associated with MLO transcript levels in mature fruits, suggesting discrete genetic control of susceptibility. These results are a critical first step in understanding allele function of MLO genes, and are necessary for further genetic studies of PM resistance in cultivated strawberry.

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Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification and Characterization of MLO Gene Family in Octoploid Strawberry (Fragaria ×ananassa)

Tapia

Barbey

Chandra

et al. 2020

Preprint

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“…Wagner (2005) suggested that there are two potential drivers of less-than-additive (Eshed and Zamir 1996) or synergistic It may be that there are few differences in protein function or expression across the three subgenomes, although this seems unlikely given mounting evidence that homeologous copies are differentially expressed in time, tissue and environment (Adams et al 2003;Liu and Adams 2007;Chaudhary et al 2009;Liu et al 2011Liu et al , 2015Pfeifer et al 2014;Zhang et al 2016;Mutti et al 2017). We were unable to assign homeologous pairs to all genes within the genome, suggesting that many of these potential sites for interacting loci were lost during polyploidization.…”

Section: Further Considerationsmentioning

confidence: 99%

Homeologous Epistasis in Wheat: The Search for an Immortal Hybrid

2019

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Hybridization between related species results in the formation of an allopolyploid with multiple subgenomes. These subgenomes will each contain complete, yet evolutionarily divergent, sets of genes. Like a diploid hybrid, allopolyploids will have two versions, or homeoalleles, for every gene. Partial functional redundancy between homeologous genes should result in a deviation from additivity. These epistatic interactions between homeoalleles are analogous to dominance effects, but are fixed across subgenomes through self pollination. An allopolyploid can be viewed as an immortalized hybrid, with the opportunity to select and fix favorable homeoallelic interactions within inbred varieties. We present a subfunctionalization epistasis model to estimate the degree of functional redundancy between homeoallelic loci and a statistical framework to determine their importance within a population. We provide an example using the homeologous dwarfing genes of allohexaploid wheat, Rht-1, and search for genome-wide patterns indicative of homeoallelic subfunctionalization in a breeding population. Using the IWGSC RefSeq v1.0 sequence, 23,796 homeoallelic gene sets were identified and anchored to the nearest DNA marker to form 10,172 homeologous marker sets. Interaction predictors constructed from products of marker scores were used to fit the homeologous main and interaction effects, as well as estimate whole genome genetic values. Some traits displayed a pattern indicative of homeoallelic subfunctionalization, while other traits showed a less clear pattern or were not affected. Using genomic prediction accuracy to evaluate importance of marker interactions, we show that homeologous interactions explain a portion of the nonadditive genetic signal, but are less important than other epistatic interactions.

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“…It may be that there are few differences in protein function or expression across the three subgenomes, although this seems unlikely given mounting evidence that homeologous copies are differentially expressed in time, tissue and environment (Adams et al ., 2003; Liu and Adams, 2007; Liu et al ., 2011; Chaudhary et al ., 2009; Pfeifer et al ., 2014; Liu et al ., 2015; Zhang et al ., 2016; Mutti et al ., 2017). We were unable to assign homeologous pairs to all genes within the genome, suggesting that many of these potential sites for interacting loci were lost during polyploidization.…”

Section: Further Considerationsmentioning

confidence: 99%

A subfunctionalization epistasis model to evaluate homeologous gene interactions in allopolyploid wheat

Santantonio

Jannink

Sorrells

2018

Preprint

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Hybridization between related species results in the formation of an allopolyploid with multiple subgenomes. These subgenomes will each contain complete, yet evolutionarily divergent, sets of genes. Like a diploid hybrid, allopolyploids will have two versions, or homeoalleles, for every gene. Partial functional redundancy between homeologous genes should result in a deviation from additivity. These epistatic interactions between homeoalleles are analogous to dominance effects, but are fixed across subgenomes through self pollination. An allopolyploid can be viewed as an immortalized hybrid, with the opportunity to select and fix favorable homeoallelic interactions within inbred varieties. We present a subfunctionalization epistasis model to estimate the degree of functional redundancy between homeoallelic loci and a statistical framework to determine their importance within a population. We provide an example using the homeologous dwarfing genes of allohexaploid wheat, Rht-1, and search for genome-wide patterns indicative of homeoallelic subfunctionalization in a breeding population. Using the IWGSC RefSeq vl.0 sequence, 23,796 homeoallelic gene sets were identified and anchored to the nearest DNA marker to form 10,172 homeologous marker sets. Interaction predictors constructed from products of marker scores were used to fit the homeologous main and interaction effects, as well as estimate whole genome genetic values. Some traits displayed a pattern indicative of homeoallelic subfunctionalization, while other traits showed a less clear pattern or were not affected. Using genomic prediction accuracy to evaluate importance of marker interactions, we show that homeologous interactions explain a portion of the non-additive genetic signal, but are less important than other epistatic interactions.

show abstract

Evolution of Gene Expression Balance Among Homeologs of Natural Polyploids

Cited by 26 publications

References 76 publications

Genome-Wide Identification and Characterization of MLO Gene Family in Octoploid Strawberry (Fragaria ×ananassa)

Genome-Wide Identification and Characterization of MLO Gene Family in Octoploid Strawberry (Fragaria ×ananassa)

Homeologous Epistasis in Wheat: The Search for an Immortal Hybrid

A subfunctionalization epistasis model to evaluate homeologous gene interactions in allopolyploid wheat

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