scholarly journals Development of chromosome-specific markers for a study on introgressive hybridization of potato with the wild Mexican allotetraploid species Solanum stoloniferum Schltdl

2020 ◽  
Vol 2 (4) ◽  
pp. 24-35
Author(s):  
O. Yu. Antonova ◽  
A. P. Yermishin ◽  
A. V. Levy ◽  
A. S. Ageeva ◽  
E. V. Voronkova ◽  
...  
Keyword(s):  
Dna Markers ◽  
Interspecific Hybrids ◽  
Genetic Material ◽  
Introgressive Hybridization ◽  
Cultivated Potato ◽  
Diploid Clone ◽  
Solanum Stoloniferum ◽  
A Genome ◽  
First Results ◽  
Cultivated Potatoes

In order to involve valuable germplasm of the wild Mexican allotetraploid potato species Solanum stoloniferum Schltdl. (genomic composition ААВВ) into breeding, pentaploid interspecific hybrids (ААAAВ) with cultivated potato S. tuberosum L. (АААА) and their backcross progenies are usually used. Homologous synapsis in meiosis of such hybrids is expected only between chromosomes of the A subgenome, therefore a question arose about a possibility of introgressing genetic material of the subgenome B into the A genome of cultivated potato. In this connection, development of various schemes for the B subgenome introgression into the genome of cultivated potato is considered as a topical issue. The previous research has yielded four schemes of S. stoloniferum involvement into breeding, which imply backcrossing with cultivated potato of the following interspecific hybrids: (1) hexaploids (genomic composition ААААВВ, the conventional introgression scheme), (2) tetraploids (putatively, АААВ), (3) self-pollination progeny of a 4x hybrid and (4) pentaploid hybrids with a putative genome composition of АААВВ. The present paper presents the first results of the development of chromosome-specific DNA markers for the identification of S. stoloniferum chromosomes in interspecific hybrids. An S. stoloniferum accession PI 205522 with a high degree of resistance to late blight and PVY had been found to possess several DNA-markers of the R-genes conferring resistance to these pathogens and was used in hybridization as a promising parent. A set of 23 SSR- and CAPS markers with the known chromosome location in S. tuberosum was generated. These markers detect polymorphism between parent genotypes, i.e., the diploid clone IGC 10/1.21 of cultivated potatoes S. tuberosum, and accession PI 205522 of S. stoloniferum. All the markers specific for the wild species were found in triploid (ААВ) and pentaploid (АААВВ) hybrids of S. stoloniferum × S. tuberosum. This set of markers will be used for efficiency assessment of different schemes for S. stoloniferum genetic material introgression into the obtained BC2-BC3 generations after crossing the interspecific hybrids with cultivated potato.

scholarly journals Production of male fertile interspecific hybrides between cultivated potatoes and valuable for breeding allotetraploid species Solanum stoloniferum

2019 ◽  
Vol 64 (2) ◽  
pp. 202-209
Author(s):  
A. V. Levy ◽  
A. S. Ageeva
Keyword(s):  
Interspecific Hybrids ◽  
Colchicine Treatment ◽  
Substantial Part ◽  
Reproductive Barriers ◽  
Solanum Stoloniferum ◽  
Fertile Pollen ◽  
Hybrid Seeds ◽  
Cultivated Potatoes ◽  
Fertile Hybrids ◽  
Allotetraploid Species

The germplasm of valuable for breeding wild allotetraploid potato species Solanum stoloniferumis rarely used because of pre- and postzygotic reproductive barriers with cultivated potatoes. One of the factors that complicate crosses between S. stoloniferum and S. tuberosumis unilateral incompatibility (UI).Here, we present the results of application of original SvSv-lines for overcoming UI in crosses with S. stoloniferum and of generating male fertile hybrids derived from this species. SvSv-lines are F2 S. tuberosum dihaploid× S. verrucosum that are male fertile and have D/γ-type cytoplasm. Since they are hybrids on homozygous for Svgene from S. verrucosum, they do not form SvSv-lines and have the same ability for elimination of prezygotic incompatibility as this species.As a result of pollination seven SvSv-lines were pollinated by 26 accessions of S. stoloniferum and a lot of hybrid seeds have been produced.In spite of low percentage of germination (1.9 %), formed 40 seedlings of interspecific hybrids. The experiment on hybridization between SvSv-lines and S. stoloniferum has been reproduced with the accession PI205522 of the wild species, which had DNA markers of PVY and LB resistance genes and “sterile” type cytoplasm W/γ: 950 hybrid seeds and 12 viable seedlings were produced. The genome of the seedlings was doubled by colchicine treatment, which generated hexaploids (F1) that formed highly fertile pollen and set seeds from self-pollination. We were able to cross them as females with the variety Katahdin. Produced pentaploid hybrids (BC1) were readily backcrossed by potato variety Quarta. Seedlings of BC2 were then backcrossed by potato varieties as female and, some of them, as male parents. The substantial part of F1, BC1 and BC2 plants of interspecific hybrids were male fertile (produced a lot functionally fertile pollen).

scholarly journals Genetic variation in recombination rate in the pig

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Martin Johnsson ◽  
Andrew Whalen ◽  
Roger Ros-Freixedes ◽  
Gregor Gorjanc ◽  
Ching-Yi Chen ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Recombination Rate ◽  
Large Scale ◽  
Genome Wide Association Study ◽  
Genetic Material ◽  
A Genome ◽  
Pig Genome ◽  
Genetic Length ◽  
Trait Locus ◽  
Genomic Regions

Abstract Background Meiotic recombination results in the exchange of genetic material between homologous chromosomes. Recombination rate varies between different parts of the genome, between individuals, and is influenced by genetics. In this paper, we assessed the genetic variation in recombination rate along the genome and between individuals in the pig using multilocus iterative peeling on 150,000 individuals across nine genotyped pedigrees. We used these data to estimate the heritability of recombination and perform a genome-wide association study of recombination in the pig. Results Our results confirmed known features of the recombination landscape of the pig genome, including differences in genetic length of chromosomes and marked sex differences. The recombination landscape was repeatable between lines, but at the same time, there were differences in average autosome-wide recombination rate between lines. The heritability of autosome-wide recombination rate was low but not zero (on average 0.07 for females and 0.05 for males). We found six genomic regions that are associated with recombination rate, among which five harbour known candidate genes involved in recombination: RNF212, SHOC1, SYCP2, MSH4 and HFM1. Conclusions Our results on the variation in recombination rate in the pig genome agree with those reported for other vertebrates, with a low but nonzero heritability, and the identification of a major quantitative trait locus for recombination rate that is homologous to that detected in several other species. This work also highlights the utility of using large-scale livestock data to understand biological processes.

Genome elimination in diploid and triploid Rana esculenta males: cytological evidence from DNA flow cytometry

Genome ◽  
1990 ◽  
Vol 33 (5) ◽  
pp. 619-627 ◽  
Author(s):  
A. E. Vinogradov ◽  
L. J. Borkin ◽  
R. Günther ◽  
J. M. Rosanov
Keyword(s):  
Flow Cytometry ◽  
Genetic Material ◽  
Rana Esculenta ◽  
Mendelian Inheritance ◽  
Study Data ◽  
Dna Flow Cytometry ◽  
Cytological Evidence ◽  
Water Frog ◽  
A Genome ◽  
Rana Lessonae

Cytological aspects of hemiclonal (meroclonal) inheritance in diploid and triploid males of the hybridogenetic frog Rana esculenta (Rana ridibunda × Rana lessonae) have been studied by DNA flow cytometry. The fact that the R. ridibunda genome contains 16% more DNA than the R. lessonae genome provides the ability to discern cells containing genomes of any species from the water-frog complex under study. Data are presented showing that elimination of the R. ridibunda genome occurs in hybridogenetic males from certain populations. In triploid males, the cytogenetic mechanism of hemiclonal inheritance is simpler than in diploids: after the elimination of a genome (always the genome in the minority in the triploid set; "homogenizing elimination"), no compensatory duplication of the remaining genetic material is necessary, as it is in diploids. The process of elimination can be visualized in triploid males by using DNA flow cytometry to identify cells in the special phase of the spermatogonial cell cycle that we termed the E phase.Key words: Rana esculenta, genome elimination, non-Mendelian inheritance, spermatogenesis, DNA flow cytometry.

scholarly journals Detection and application of genome-wide variations in peach for association and genetic relationship analysis

BMC Genetics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Liping Guan ◽  
Ke Cao ◽  
Yong Li ◽  
Jian Guo ◽  
Qiang Xu ◽  
...  
Keyword(s):  
Genetic Relationship ◽  
Dna Markers ◽  
High Throughput Sequencing ◽  
Prunus Persica ◽  
Genetic Research ◽  
Diploid Species ◽  
Sequencing Data ◽  
Relationship Analysis ◽  
Genome Wide ◽  
A Genome

Abstract Background Peach (Prunus persica L.) is a diploid species and model plant of the Rosaceae family. In the past decade, significant progress has been made in peach genetic research via DNA markers, but the number of these markers remains limited. Results In this study, we performed a genome-wide DNA markers detection based on sequencing data of six distantly related peach accessions. A total of 650,693~1,053,547 single nucleotide polymorphisms (SNPs), 114,227~178,968 small insertion/deletions (InDels), 8386~12,298 structure variants (SVs), 2111~2581 copy number variants (CNVs) and 229,357~346,940 simple sequence repeats (SSRs) were detected and annotated. To demonstrate the application of DNA markers, 944 SNPs were filtered for association study of fruit ripening time and 15 highly polymorphic SSRs were selected to analyze the genetic relationship among 221 accessions. Conclusions The results showed that the use of high-throughput sequencing to develop DNA markers is fast and effective. Comprehensive identification of DNA markers, including SVs and SSRs, would be of benefit to genetic diversity evaluation, genetic mapping, and molecular breeding of peach.

Screening of Wild Potatoes Identifies New Sources of Late Blight Resistance

Plant Disease ◽  
2020 ◽  
pp. PDIS-06-20-1367 ◽  
Author(s):  
Hari S. Karki ◽  
Shelly H. Jansky ◽  
Dennis A. Halterman
Keyword(s):  
Late Blight ◽  
Late Blight Resistance ◽  
Wild Relatives ◽  
Plant Diseases ◽  
Clonal Lineage ◽  
Wild Potato Species ◽  
Detached Leaf ◽  
Solanum Stoloniferum ◽  
Cultivated Potatoes ◽  
Excellent Source

Late blight (LB) of potato is considered one of the most devastating plant diseases in the world. Most cultivated potatoes are susceptible to this disease. However, wild relatives of potatoes are an excellent source of LB resistance. We screened 384 accessions of 72 different wild potato species available from the U.S. Potato GeneBank against the LB pathogen Phytophthora infestans in a detached leaf assay (DLA). P. infestans isolates US-23 and NL13316 were used in the DLA to screen the accessions. Although all plants in 273 accessions were susceptible, all screened plants in 39 accessions were resistant. Resistant and susceptible plants were found in 33 accessions. All tested plants showed a partial resistance phenotype in two accessions, segregation of resistant and partial resistant plants in nine accessions, segregation of partially resistant and susceptible plants in four accessions, and segregation of resistant, partially resistant, and susceptible individuals in 24 accessions. We found several species that were never before reported to be resistant to LB: Solanum albornozii, S. agrimoniifolium, S. chomatophilum, S. ehrenbergii, S. hypacrarthrum, S. iopetalum, S. palustre, S. piurae, S. morelliforme, S. neocardenasii, S. trifidum, and S. stipuloideum. These new species could provide novel sources of LB resistance. P. infestans clonal lineage-specific screening of selected species was conducted to identify the presence of RB resistance. We found LB resistant accessions in Solanum verrucosum, Solanum stoloniferum, and S. morelliforme that were susceptible to the RB overcoming isolate NL13316, indicating the presence of RB-like resistance in these species.

Construction of chromosomal recombination maps of three genomes of lilies (Lilium) based on GISH analysis

Genome ◽  
2009 ◽  
Vol 52 (3) ◽  
pp. 238-251 ◽  
Author(s):  
Nadeem Khan ◽  
Rodrigo Barba-Gonzalez ◽  
M. S. Ramanna ◽  
Richard G.F. Visser ◽  
Jaap M. Van Tuyl
Keyword(s):  
Molecular Markers ◽  
Interspecific Hybrids ◽  
The Other ◽  
A Genome ◽  
Chromosomal Recombination ◽  
Gish Analysis ◽  
The Way

Chromosomal recombination maps were constructed for three genomes of lily ( Lilium ) using GISH analyses. For this purpose, the backcross (BC) progenies of two diploid (2n = 2x = 24) interspecific hybrids of lily, viz. Longiflorum × Asiatic (LA) and Oriental × Asiatic (OA), were used. Mostly the BC progenies of LA hybrids consisted of both triploid (2n = 3x = 36) and diploid (2n = 2x = 24) with some aneuploid genotypes and those of OA hybrids consisted of triploid (2n = 3x = 36) and some aneuploid genotypes. In all cases, it was possible to identify the homoeologous recombinant chromosomes as well as accurately count the number of crossover points, which are called “recombination sites”. Recombination sites were estimated in the BC progeny of 71 LA and 41 OA genotypes. In the case of BC progenies of LA hybrids, 248 recombination sites were cytologically localized on 12 different chromosomes of each genome (i.e., L and A). Similarly, 116 recombinant sites were localized on the 12 chromosomes each from the BC progenies of OA hybrids (O and A genomes). Cytological maps were constructed on the basis of the percentages of distances (micrometres) of the recombination sites from the centromeres. Since an Asiatic parent was involved in both hybrids, viz. LA and OA, two maps were constructed for the A genome that were indicated as Asiatic (L) and Asiatic (O). The other two maps were Longiflorum (A) and Oriental (A). Remarkably, the recombination sites were highly unevenly distributed among the different chromosomes of all four maps. Because the recombination sites can be unequivocally identified through GISH, they serve as reliable landmarks and pave the way for assigning molecular markers or desirable genes to chromosomes of Lilium and also monitor introgression of alien segments.

scholarly journals Extensive Recombination-Induced Disruption of Genetic Interactions Is Highly Deleterious but Can Be Partially Reversed by Small Numbers of Secondary Recombination Events

2014 ◽  
Vol 88 (14) ◽  
pp. 7843-7851 ◽  
Author(s):  
Adérito L. Monjane ◽  
Darren P. Martin ◽  
Francisco Lakay ◽  
Brejnev M. Muhire ◽  
Daniel Pande ◽  
...  
Keyword(s):  
Genetic Material ◽  
Evolutionary Process ◽  
Virus Genome ◽  
Maize Streak Virus ◽  
Genetic Interactions ◽  
Streak Virus ◽  
Fitness Costs ◽  
A Genome ◽  
Virus Genomes ◽  
Recombination Breakpoints

ABSTRACTAlthough homologous recombination can potentially provide viruses with vastly more evolutionary options than are available through mutation alone, there are considerable limits on the adaptive potential of this important evolutionary process. Primary among these is the disruption of favorable coevolved genetic interactions that can occur following the transfer of foreign genetic material into a genome. Although the fitness costs of such disruptions can be severe, in some cases they can be rapidly recouped by either compensatory mutations or secondary recombination events. Here, we used a maize streak virus (MSV) experimental model to explore both the extremes of recombination-induced genetic disruption and the capacity of secondary recombination to adaptively reverse almost lethal recombination events. Starting with two naturally occurring parental viruses, we synthesized two of the most extreme conceivable MSV chimeras, each effectively carrying 182 recombination breakpoints and containing thorough reciprocal mixtures of parental polymorphisms. Although both chimeras were severely defective and apparently noninfectious, neither had individual movement-, encapsidation-, or replication-associated genome regions that were on their own “lethally recombinant.” Surprisingly, mixed inoculations of the chimeras yielded symptomatic infections with viruses with secondary recombination events. These recombinants had only 2 to 6 breakpoints, had predominantly inherited the least defective of the chimeric parental genome fragments, and were obviously far more fit than their synthetic parents. It is clearly evident, therefore, that even when recombinationally disrupted virus genomes have extremely low fitness and there are no easily accessible routes to full recovery, small numbers of secondary recombination events can still yield tremendous fitness gains.IMPORTANCERecombination between viruses can generate strains with enhanced pathological properties but also runs the risk of producing hybrid genomes with decreased fitness due to the disruption of favorable genetic interactions. Using two synthetic maize streak virus genome chimeras containing alternating genome segments derived from two natural viral strains, we examined both the fitness costs of extreme degrees of recombination (both chimeras had 182 recombination breakpoints) and the capacity of secondary recombination events to recoup these costs. After the severely defective chimeras were introduced together into a suitable host, viruses with between 1 and 3 secondary recombination events arose, which had greatly increased replication and infective capacities. This indicates that even in extreme cases where recombination-induced genetic disruptions are almost lethal, and 91 consecutive secondary recombination events would be required to reconstitute either one of the parental viruses, moderate degrees of fitness recovery can be achieved through relatively small numbers of secondary recombination events.

scholarly journals Divergence-Based Introgression Polarization

2020 ◽  
Vol 12 (4) ◽  
pp. 463-478 ◽  
Author(s):  
Evan S Forsythe ◽  
Daniel B Sloan ◽  
Mark A Beilstein
Keyword(s):  
Genetic Material ◽  
Introgressive Hybridization ◽  
Sequence Divergence ◽  
Whole Genome ◽  
Major Area ◽  
Genome Data ◽  
Whole Genomes ◽  
Potential Sources ◽  
Introgression Event ◽  
Do So

Abstract Introgressive hybridization results in the transfer of genetic material between species, often with fitness implications for the recipient species. The development of statistical methods for detecting the signatures of historical introgression in whole-genome data has been a major area of focus. Although existing techniques are able to identify the taxa that exchanged genes during introgression using a four-taxon system, most methods do not explicitly distinguish which taxon served as donor and which as recipient during introgression (i.e., polarization of introgression directionality). Existing methods that do polarize introgression are often only able to do so when there is a fifth taxon available and that taxon is sister to one of the taxa involved in introgression. Here, we present divergence-based introgression polarization (DIP), a method for polarizing introgression using patterns of sequence divergence across whole genomes, which operates in a four-taxon context. Thus, DIP can be applied to infer the directionality of introgression when additional taxa are not available. We use simulations to show that DIP can polarize introgression and identify potential sources of bias in the assignment of directionality, and we apply DIP to a well-described hominin introgression event.

Perspectives in chromosome manipulation

1981 ◽  
Vol 292 (1062) ◽  
pp. 535-546 ◽  
Keyword(s):  
Male Sterility ◽  
Fertility Restoration ◽  
Genetic Material ◽  
Diploid Wheat ◽  
Translocation Chromosome ◽  
Chromosome 4 ◽  
Genome Chromosome ◽  
Genetic Components ◽  
A Genome ◽  
Chromosome Manipulation

Three categories of chromosome manipulation are discussed, with examples from hexaploid wheat. First, uncontrolled events, such as intergeneric translocations induced by mutagenic agents, have been frequently isolated but have been infrequently incorporated into widely grown varieties. A method proposed by K. W. Shepherd is designed to select an accommodating genetic background for these interchanges and thereby overcome this deficiency. This relies on selection for yield among many selections that are homozygous for a translocation but segregating for many other genetic components. The second category involves manipulations associated with the distinctive genetic activity of chromosome 5B. ph mutants are expected to play an important role in the transfer of genetic material from other genera to wheat. A method described by E. R. Sears is designed to isolate a small intercalated alien segment. This relies on crossing-over in an alien segment that is common to two distinct types of homoeologous-exchange chromosomes. The third category involves manipulations associated with a male-sterility mutation on chromosome 4A and the distinctive genetic activities of this chromosome. A method, described by the author, is designed to produce hybrid wheat with an induced male-sterility mutation on this chromosome. Fertility restoration is being attempted with four chromosomes, a restriction on which is that they must not pair with the other chromosomes of the wheat complement. These are a modified 4A -2R translocation chromosome, part of the cereal rye genome, chromosome 4 of barley, and chromosome 4 of diploid wheat. It appears that chromosome 4A originated elsewhere than from diploid wheat; thus the A genome of common wheat arose from at least two species. As detected by M. A. Hossain and the author, part of the genetic material for male fertility on 4A has a counterpart on rye chromosome 2R. An exchange between the chromosomes of homoeologous groups 2 and 4 appears to have occurred, perhaps at the diploid level.

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