The plasmon-genic basis of pollen lobedness and tetrad sterility in Solanum verrucosum hybrids and duplicate linkage groups

Accelerated improvement of two cornerstones of New Zealand's pastoral industries, per ennial ryegrass (Lolium perenne L.) and white clover (Trifolium repens L.), may be realised through the application of markerassisted selection (MAS) strategies to enhance traditional plant breeding programmes. Genome maps constructed using molecular markers represent the enabling technology for such strategies and we have assembled maps for each species using EST-SSR markers - simple sequence repeat (SSR) markers developed from expressed sequence tags (ESTs) representing genes. A comprehensive map of the white clover genome has been completed, with 464 EST-SSR and genomic SSR marker loci spanning 1125 cM in total, distributed across 16 linkage groups. These have been further classified into eight pairs of linkage groups, representing contributions from the diploid progenitors of this tetraploid species. In perennial ryegrass a genome map based exclusively on EST-SSR loci was constructed, with 130 loci currently mapped to seven linkage groups and covering a distance of 391 cM. This map continues to be expanded with the addition of ESTSSR loci, and markers are being concurrently transferred to other populations segregating for economically significant traits. We have initiated gene discovery through quantitative trait locus (QTL) analysis in both species, and the efficacy of the white clover map for this purpose was demonstrated with the initial identification of multiple QTL controlling seed yield and seedling vigour. One QTL on linkage group D2 accounts for 25.9% of the genetic variation for seed yield, and a putative QTL accounting for 12.7% of the genetic variation for seedling vigour was detected on linkage group E1. The application of MAS to forage breeding based on recurrent selection is discussed. Keywords: genome map, marker-assisted selection, perennial ryegrass, QTL, quantitative trait locus, SSR, simple sequence repeat, white clover

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Secondary Trisomics and Telotrisomics of Rice: Origin, Characterization, and Use in Determining the Orientation of Chromosome Map

Genetics ◽

10.1093/genetics/143.1.517 ◽

1996 ◽

Vol 143 (1) ◽

pp. 517-529

Author(s):

Kuldeep Singh ◽

D S Multani ◽

Gurdev S Khush

Keyword(s):

Linkage Map ◽

Large Population ◽

Marker Genes ◽

Linkage Groups ◽

Breeding Behavior ◽

Specific Chromosome ◽

Chromosome Map ◽

Primary Trisomics ◽

Correct Orientation ◽

Genetic Segregation

Abstract Secondary trisomics and telotrisomics representing the 12 chromosomes of rice were isolated from the progenies of primary trisomics. A large population of each primary trisomic was grown. Plants showing variation in gross morphology compared to the primary trisomics and disomic sibs were selected and analyzed cytologically at diakinesis and pachytene. Secondary trisomics for both arms of chromosomes 1, 2, 6, 7 and 11 and for one arm of chromosomes 4, 5, 8, 9 and 12 were identified. Telotrisomics for short arm of chromosomes 1, 8, 9 and 10 and for long arms of chromosomes 2, 3 and 5 were isolated. These secondary and telotrisomics were characterized morphologically and for breeding behavior. Secondary trisomics 2n + 1S · 1S, 2n + 1L · 1L, 2n + 2S · 2S, 2n + 2L · 2L, 2n + 6S · 6S, 2n + 6L · 6L and 2n + 7L · 7L are highly sterile, and 2n + 1L · 1L, 2n + 2L · 2L and 2n + 7L · 7L do not set any seed even upon backcrossing. Telotrisomics are fertile and vigorous. Genetic segregation of 43 marker genes was studied in the F2 or backcross progenies. On the basis of segregation data, these genes were delimited to specific chromosome arms. Correct orientation of 10 linkage groups was determined and centromere positions on nine linkage groups were approximated. A revised linkage map of rice is presented.

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Analysis and Mapping of Gene Families Encoding β-1,3-Glucanases of Soybean

Genetics ◽

10.1093/genetics/153.1.445 ◽

1999 ◽

Vol 153 (1) ◽

pp. 445-452

Author(s):

Wei Jin ◽

Harry T Horner ◽

Reid G Palmer ◽

Randy C Shoemaker

Keyword(s):

Gene Families ◽

Mrna Levels ◽

Linkage Groups ◽

Flower Bud ◽

Cross Hybridization ◽

Coding Regions ◽

F2 Population ◽

Young Leaves ◽

Glycine Max L ◽

Stem Leaf

Abstract Oligonucleotide primers designed for conserved sequences from coding regions of β-1,3-glucanase genes from different species were used to amplify related sequences from soybean [Glycine max (L.) Merr.]. Sequencing and cross-hybridization of amplification products indicated that at least 12 classes of β-1,3-glucanase genes exist in the soybean. Members of classes mapped to 34 loci on five different linkage groups using an F2 population of 56 individuals. β-1,3-Glucanase genes are clustered onto regions of five linkage groups. Data suggest that more closely related genes are clustered together on one linkage group or on duplicated regions of linkage groups. Northern blot analyses performed on total RNA from root, stem, leaf, pod, flower bud, and hypocotyl using DNA probes for the different classes of β-1,3-glucanase genes revealed that the mRNA levels of all classes were low in young leaves. SGlu2, SGlu4, SGlu7, and SGlu12 mRNA were highly accumulated in young roots and hypocotyls. SGlu7 mRNA also accumulated in pods and flower buds.

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Chromosomal Map of the Model LegumeLotus japonicus

Genetics ◽

10.1093/genetics/161.4.1661 ◽

2002 ◽

Vol 161 (4) ◽

pp. 1661-1672 ◽

Cited By ~ 7

Author(s):

Andrea Pedrosa ◽

Niels Sandal ◽

Jens Stougaard ◽

Dieter Schweizer ◽

Andreas Bachmair

Keyword(s):

Repetitive Sequences ◽

Lotus Japonicus ◽

Chromosome Complement ◽

Linkage Groups ◽

Closely Related Species ◽

F1 Hybrid ◽

Bac Clones ◽

Genomic Regions ◽

Chromosomal Map

AbstractLotus japonicus is a model plant for the legume family. To facilitate map-based cloning approaches and genome analysis, we performed an extensive characterization of the chromosome complement of the species. A detailed karyotype of L. japonicus Gifu was built and plasmid and BAC clones, corresponding to genetically mapped markers (see the accompanying article by Sandal et al. 2002, this issue), were used for FISH to correlate genetic and chromosomal maps. Hybridization of DNA clones from 32 different genomic regions enabled the assignment of linkage groups to chromosomes, the comparison between genetic and physical distances throughout the genome, and the partial characterization of different repetitive sequences, including telomeric and centromeric repeats. Additional analysis of L. filicaulis and its F1 hybrid with L. japonicus demonstrated the occurrence of inversions between these closely related species, suggesting that these chromosome rearrangements are early events in speciation of this group.

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Adaptive Divergence under Gene Flow along an Environmental Gradient in Two Coexisting Stickleback Species

Genes ◽

10.3390/genes12030435 ◽

2021 ◽

Vol 12 (3) ◽

pp. 435

Author(s):

Thijs M. P. Bal ◽

Alejandro Llanos-Garrido ◽

Anurag Chaturvedi ◽

Io Verdonck ◽

Bart Hellemans ◽

...

Keyword(s):

Gene Flow ◽

Brackish Water ◽

Environmental Gradient ◽

Spatial Scales ◽

Morphological Differentiation ◽

Genotyping By Sequencing ◽

Adaptive Divergence ◽

Linkage Groups ◽

Closely Related Species ◽

Genomic Patterns

There is a general and solid theoretical framework to explain how the interplay between natural selection and gene flow affects local adaptation. Yet, to what extent coexisting closely related species evolve collectively or show distinctive evolutionary responses remains a fundamental question. To address this, we studied the population genetic structure and morphological differentiation of sympatric three-spined and nine-spined stickleback. We conducted genotyping-by-sequencing and morphological trait characterisation using 24 individuals of each species from four lowland brackish water (LBW), four lowland freshwater (LFW) and three upland freshwater (UFW) sites in Belgium and the Netherlands. This combination of sites allowed us to contrast populations from isolated but environmentally similar locations (LFW vs. UFW), isolated but environmentally heterogeneous locations (LBW vs. UFW), and well-connected but environmentally heterogenous locations (LBW vs. LFW). Overall, both species showed comparable levels of genetic diversity and neutral genetic differentiation. However, for all three spatial scales, signatures of morphological and genomic adaptive divergence were substantially stronger among populations of the three-spined stickleback than among populations of the nine-spined stickleback. Furthermore, most outlier SNPs in the two species were associated with local freshwater sites. The few outlier SNPs that were associated with the split between brackish water and freshwater populations were located on one linkage group in three-spined stickleback and two linkage groups in nine-spined stickleback. We conclude that while both species show congruent evolutionary and genomic patterns of divergent selection, both species differ in the magnitude of their response to selection regardless of the geographical and environmental context.

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Linkage group XIX of Chlamydomonas reinhardtii has a linear map.

Genetics ◽

10.1093/genetics/133.4.865 ◽

1993 ◽

Vol 133 (4) ◽

pp. 865-874

Author(s):

J A Holmes ◽

D E Johnson ◽

S K Dutcher

Keyword(s):

Linkage Group ◽

Chlamydomonas Reinhardtii ◽

Mutant Strain ◽

Meiotic Recombination ◽

Temperature Sensitive ◽

Unusual Property ◽

Linkage Groups ◽

Excess Number ◽

Chiasma Interference ◽

Double Crossovers

Abstract Linkage group XIX (or the UNI linkage group) of Chlamydomonas reinhardtii has been reported to show a circular meiotic recombination map. A circular map predicts the existence of strong chiasma and chromatid interference, which would lead to an excess number of two-strand double crossovers during meiosis. We have tested this prediction in multipoint crosses. Our results are consistent with a linear linkage group that shows positive chiasma interference and no chromatid interference. Chiasma interference occurs both within arms and across the centromere. Of the original loci that contributed to the circular map, we find that two map to other linkage groups and a third cannot be retested because the mutant strain that defined it has been lost. A second reported unusual property for linkage group XIX was the increase in meiotic recombination with increases in temperature during a period that precedes the onset of meiosis. Although we observed changes in recombination frequencies in some intervals on linkage group XIX in crosses to CC-1952, and in strains heterozygous for the mutation ger1 at 16 degrees, we also show that our strains do not exhibit the previously observed patterns of temperature-sensitive recombination for two different pairs of loci on linkage group XIX. We conclude that linkage group XIX has a linear genetic map that is not significantly different from other Chlamydomonas linkage groups.

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Genome Duplication in Soybean (Glycine subgenus soja)

Genetics ◽

10.1093/genetics/144.1.329 ◽

1996 ◽

Vol 144 (1) ◽

pp. 329-338 ◽

Cited By ~ 6

Author(s):

R C Shoemaker ◽

K Polzin ◽

J Labate ◽

J Specht ◽

E C Brummer ◽

...

Keyword(s):

Seed Protein ◽

Genome Duplication ◽

Fragment Length Polymorphism ◽

Gene Families ◽

Soybean Genome ◽

Seed Composition ◽

Linkage Groups ◽

Mapping Data ◽

Or Gene ◽

Average Size

Abstract Restriction fragment length polymorphism mapping data from nine populations (Glycine max × G. soja and G. max × G. max) of the Glycine subgenus soja genome led to the identification of many duplicated segments of the genome. Linkage groups contained up to 33 markers that were duplicated on other linkage groups. The size of homoeologous regions ranged from 1.5 to 106.4 cM, with an average size of 45.3 cM. We observed segments in the soybean genome that were present in as many as six copies with an average of 2.55 duplications per segment. The presence of nested duplications suggests that at least one of the original genomes may have undergone an additional round of tetraploidization. Tetraploidization, along with large internal duplications, accounts for the highly duplicated nature of the genome of the subgenus. Quantitative trait loci for seed protein and oil showed correspondence across homoeologous regions, suggesting that the genes or gene families contributing to seed composition have retained similar functions throughout the evolution of the chromosomes.

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A Genetic Map of Gibberella fujikuroi Mating Population A (Fusarium moniliforme)

Genetics ◽

10.1093/genetics/143.1.175 ◽

1996 ◽

Vol 143 (1) ◽

pp. 175-189 ◽

Cited By ~ 2

Author(s):

Jin-rong Xu ◽

John F Leslie

Keyword(s):

Fusarium Moniliforme ◽

Fragment Length Polymorphism ◽

Fumonisin B1 ◽

Gibberella Fujikuroi ◽

Female Sterility ◽

Rflp Markers ◽

Linkage Groups ◽

Mating Population ◽

Spore Killer ◽

Chiasma Interference

Abstract We constructed a recombination-based map of the fungal plant pathogen Gibberella fujikuroi mating population A (asexual stage Fusarium moniliforme). The map is based on the segregation of 142 restriction fragment length polymorphism (RFLP) markers, two auxotrophic genes (arg1, nic1), mating type (matA+ / matA−), female sterility (ste1), spore-killer (Sk), and a gene governing the production of the mycotoxin fumonisin B1 (fum1) among 121 random ascospore progeny from a single cross. We identified 12 linkage groups corresponding to the 12 chromosome-sized DNAs previously observed in contour-clamped homogeneous electric field (CHEF) gels. Linkage groups and chromosomes were correlated via Southern blots between appropriate RFLP markers and the CHEF gels. Eleven of the 12 chromosomes are meiotically stable, but the 12th (and smallest) is subject to deletions in 3% (4/121) of the progeny. Positive chiasma interference occurred on five of the 12 chromosomes, and nine of the 12 chromosomes averaged more than one crossover per chromosome. The average kb/cM ratio in this cross is ~32.

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QTL analysis of seed germination traits in tobacco (Nicotiana tabacum L.)

Journal of Applied Genetics ◽

10.1007/s13353-021-00623-6 ◽

2021 ◽

Author(s):

Monika Agacka-Mołdoch ◽

Mian Abdur Rehman Arif ◽

Ulrike Lohwasser ◽

Teresa Doroszewska ◽

Ramsey S. Lewis ◽

...

Keyword(s):

Nicotiana Tabacum ◽

Seed Germination ◽

Doubled Haploid ◽

Mapping Population ◽

Area Under The Curve ◽

Linkage Groups ◽

Polygenic Control ◽

Nicotiana Tabacum L ◽

Controlled Deterioration ◽

Germination Traits

AbstractGenetic mapping of seed germination traits has been performed with many plant species. In tobacco, however, investigations are rare. In the present study, a bi-parental mapping population consisting of 118 doubled haploid lines and derived from a cross between ‘Beinhart-1000’ and ‘Hicks’ was investigated. Four germination-related traits, total germination (TG), normal germination (NG), time to reach 50% of total germination (T50), and the area under the curve after 200 h of germination (AUC) were considered by examining seeds either untreated or after a moderate controlled deterioration (CD). Quantitative trait loci were found for all traits distributed on 11 out of the 24 linkage groups. It was demonstrated that, as in many other species, germination-related traits are very complex and under polygenic control.

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An enhanced molecular marker based genetic map of perennial ryegrass (Lolium perenne) reveals comparative relationships with other Poaceae genomes

Genome ◽

10.1139/g01-144 ◽

2002 ◽

Vol 45 (2) ◽

pp. 282-295 ◽

Cited By ~ 175

Author(s):

Elizabeth S Jones ◽

Natalia L Mahoney ◽

Michael D Hayward ◽

Ian P Armstead ◽

J Gilbert Jones ◽

...

Keyword(s):

Molecular Marker ◽

Linkage Map ◽

Genetic Map ◽

Lolium Perenne ◽

Perennial Ryegrass ◽

Genetic Linkage Map ◽

Population Based ◽

Genetic Maps ◽

Linkage Groups ◽

Integrated Genetic Map

A molecular-marker linkage map has been constructed for perennial ryegrass (Lolium perenne L.) using a one-way pseudo-testcross population based on the mating of a multiple heterozygous individual with a doubled haploid genotype. RFLP, AFLP, isoenzyme, and EST data from four collaborating laboratories within the International Lolium Genome Initiative were combined to produce an integrated genetic map containing 240 loci covering 811 cM on seven linkage groups. The map contained 124 codominant markers, of which 109 were heterologous anchor RFLP probes from wheat, barley, oat, and rice, allowing comparative relationships between perennial ryegrass and other Poaceae species to be inferred. The genetic maps of perennial ryegrass and the Triticeae cereals are highly conserved in terms of synteny and colinearity. This observation was supported by the general agreement of the syntenic relationships between perennial ryegrass, oat, and rice and those between the Triticeae and these species. A lower level of synteny and colinearity was observed between perennial ryegrass and oat compared with the Triticeae, despite the closer taxonomic affinity between these species. It is proposed that the linkage groups of perennial ryegrass be numbered in accordance with these syntenic relationships, to correspond to the homoeologous groups of the Triticeae cereals.Key words: Lolium perenne, genetic linkage map, RFLP, AFLP, conserved synteny.

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