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      Homoeologous recombination is recurrent in the nascent synthetic allotetraploid Arachis ipaënsis × Arachis correntina 4x and its derivatives

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          Abstract

          Genome instability in newly synthesized allotetraploids of peanut has breeding implications that have not been fully appreciated. Synthesis of wild species-derived neo-tetraploids offers the opportunity to broaden the gene pool of peanut; however, the dynamics among the newly merged genomes creates predictable and unpredictable variation. Selfed progenies from the neo-tetraploid Arachis ipaënsis × Arachis correntina ( A. ipaënsis × A. correntina) 4x and F 1 hybrids and F 2 progenies from crosses between A. hypogaea × [ A. ipaënsis × A. correntina] 4x were genotyped by the Axiom Arachis 48 K SNP array. Homoeologous recombination between the A. ipaënsis and A. correntina derived subgenomes was observed in the S 0 generation. Among the S 1 progenies, these recombined segments segregated and new events of homoeologous recombination emerged. The genomic regions undergoing homoeologous recombination segregated mostly disomically in the F 2 progenies from A. hypogaea × [ A. ipaënsis × A. correntina] 4x crosses. New homoeologous recombination events also occurred in the F 2 population, mostly found on chromosomes 03, 04, 05, and 06. From the breeding perspective, these phenomena offer both possibilities and perils; recombination between genomes increases genetic diversity, but genome instability could lead to instability of traits or even loss of viability within lineages.

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          The genome sequence of segmental allotetraploid peanut Arachis hypogaea

          Like many other crops, the cultivated peanut (Arachis hypogaea L.) is of hybrid origin and has a polyploid genome that contains essentially complete sets of chromosomes from two ancestral species. Here we report the genome sequence of peanut and show that after its polyploid origin, the genome has evolved through mobile-element activity, deletions and by the flow of genetic information between corresponding ancestral chromosomes (that is, homeologous recombination). Uniformity of patterns of homeologous recombination at the ends of chromosomes favors a single origin for cultivated peanut and its wild counterpart A. monticola. However, through much of the genome, homeologous recombination has created diversity. Using new polyploid hybrids made from the ancestral species, we show how this can generate phenotypic changes such as spontaneous changes in the color of the flowers. We suggest that diversity generated by these genetic mechanisms helped to favor the domestication of the polyploid A. hypogaea over other diploid Arachis species cultivated by humans.
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            The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut.

            Cultivated peanut (Arachis hypogaea) is an allotetraploid with closely related subgenomes of a total size of ∼2.7 Gb. This makes the assembly of chromosomal pseudomolecules very challenging. As a foundation to understanding the genome of cultivated peanut, we report the genome sequences of its diploid ancestors (Arachis duranensis and Arachis ipaensis). We show that these genomes are similar to cultivated peanut's A and B subgenomes and use them to identify candidate disease resistance genes, to guide tetraploid transcript assemblies and to detect genetic exchange between cultivated peanut's subgenomes. On the basis of remarkably high DNA identity of the A. ipaensis genome and the B subgenome of cultivated peanut and biogeographic evidence, we conclude that A. ipaensis may be a direct descendant of the same population that contributed the B subgenome to cultivated peanut.
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              Patterns of sequence loss and cytosine methylation within a population of newly resynthesized Brassica napus allopolyploids.

              Allopolyploid formation requires the adaptation of two nuclear genomes within a single cytoplasm, which may involve programmed genetic and epigenetic changes during the initial generations following genome fusion. To study the dynamics of genome change, we synthesized 49 isogenic Brassica napus allopolyploids and surveyed them with 76 restriction fragment length polymorphism (RFLP) probes and 30 simple sequence repeat (SSR) primer pairs. Here, we report on the types and distribution of genetic and epigenetic changes within the S(1) genotypes. We found that insertion/deletion (indel) events were rare, but not random. Of the 57,710 (54,383 RFLP and 3,327 SSR) parental fragments expected among the amphidiploids, we observed 56,676 or 99.9%. Three loci derived from Brassica rapa had indels, and one indel occurred repeatedly across 29% (14/49) of the lines. Loss of one parental fragment was due to the 400-bp reduction of a guanine-adenine dinucleotide repeat-rich sequence. In contrast to the 4% (3/76) RFLP probes that detected indels, 48% (35/73) detected changes in the CpG methylation status between parental genomes and the S1 lines. Some loci were far more likely than others to undergo epigenetic change, but the number of methylation changes within each synthetic polyploid was remarkably similar to others. Clear de novo methylation occurred at a much higher frequency than de novo demethylation within allopolyploid sequences derived from B. rapa. Our results suggest that there is little genetic change in the S(0) generation of resynthesized B. napus polyploids. In contrast, DNA methylation was altered extensively in a pattern that indicates tight regulation of epigenetic changes.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                G3 (Bethesda)
                Genetics
                g3journal
                G3: Genes|Genomes|Genetics
                Oxford University Press
                2160-1836
                April 2021
                08 March 2021
                08 March 2021
                : 11
                : 4
                : jkab066
                Affiliations
                [1 ]Horticulture Department, University of Georgia , Tifton, GA 31793, USA
                [2 ]Center for Applied Genetic Technologies, University of Georgia , Athens, GA 30602, USA
                [3 ]Institute of Plant Breeding, Genetics and Genomics, University of Georgia , Athens, GA 30602, USA
                [4 ]Department of Crop and Soil Science, University of Georgia , Athens, GA 30602, USA
                [5 ]Department of Crop and Soil Sciences, North Carolina State University , Raleigh, NC 27695, USA
                [6 ]USDA- Agricultural Research Service, Crop Genetics and Breeding Research Unit , Tifton, GA 31793, USA
                Author notes
                Corresponding author: Rm 107 NESPAL, 2356 Rainwater Road, Tifton, GA 31793, USA. pozias@ 123456uga.edu
                Author information
                https://orcid.org/0000-0002-8977-7945
                Article
                jkab066
                10.1093/g3journal/jkab066
                8759810
                33693764
                d6f710d5-885b-4ca5-a467-9b3ca98084e2
                © The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs licence ( http://creativecommons.org/licenses/by-nc-nd/4.0/), which permits non-commercial reproduction and distribution of the work, in any medium, provided the original work is not altered or transformed in any way, and that the work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

                History
                : 03 December 2020
                : 21 February 2021
                Page count
                Pages: 13
                Funding
                Funded by: National Science Foundation, DOI 10.13039/100000001;
                Award ID: MCB-1543922
                Funded by: AFRI NIFA Fellowships Grant Program: Predoctoral Fellowship;
                Award ID: 1019105
                Funded by: USDA National Institute of Food and Agriculture;
                Categories
                Genome Reports
                AcademicSubjects/SCI01180
                AcademicSubjects/SCI01140
                AcademicSubjects/SCI00010
                AcademicSubjects/SCI00960

                Genetics
                arachis hypogaea (peanut),homoeologous recombination,synthetic allotetraploid,a. ipaënsis,a. correntina

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