scholarly journals Genome sequencing of the Australian wild diploid species Gossypium australe highlights disease resistance and delayed gland morphogenesis

2019 ◽  
Vol 18 (3) ◽  
pp. 814-828 ◽  
Author(s):  
Yingfan Cai ◽  
Xiaoyan Cai ◽  
Qinglian Wang ◽  
Ping Wang ◽  
Yu Zhang ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Genome Sequencing ◽  
Diploid Species ◽  
Gland Morphogenesis ◽  
Wild Diploid Species

A Centromeric Tandem Repeat Family Originating From a Part of Ty3/gypsy-Retroelement in Wheat and Its Relatives

Genetics ◽  
2003 ◽  
Vol 164 (2) ◽  
pp. 665-672 ◽  
Author(s):  
Zhi-Jun Cheng ◽  
Minoru Murata
Keyword(s):  
In Situ Hybridization ◽  
Tandem Repeats ◽  
Diploid Species ◽  
Upstream Region ◽  
Aegilops Speltoides ◽  
Repeat Family ◽  
B Genome ◽  
Intervening Sequences ◽  
Wild Diploid Species

AbstractFrom a wild diploid species that is a relative of wheat, Aegilops speltoides, a 301-bp repeat containing 16 copies of a CAA microsatellite was isolated. Southern blot and fluorescence in situ hybridization revealed that ∼250 bp of the sequence is tandemly arrayed at the centromere regions of A- and B-genome chromosomes of common wheat and rye chromosomes. Although the DNA sequence of this 250-bp repeat showed no notable homology in the databases, the flanking or intervening sequences between the repeats showed high homologies (>82%) to two separate sequences of the gag gene and its upstream region in cereba, a Ty3/gypsy-like retroelement of Hordeum vulgare. Since the amino acid sequence deduced from the 250 bp with seven CAAs showed some similarity (∼53%) to that of the gag gene, we concluded that the 250-bp repeats had also originated from the cereba-like retroelements in diploid wheat such as Ae. speltoides and had formed tandem arrays, whereas the 300-bp repeats were dispersed as a part of cereba-like retroelements. This suggests that some tandem repeats localized at the centromeric regions of cereals and other plant species originated from parts of retrotransposons.

scholarly journals Identification of Rare Recombinants Leads to Tightly Linked Markers for Nematode Resistance in Peanut

2016 ◽  
Vol 43 (2) ◽  
pp. 88-93 ◽  
Author(s):  
Y. Chu ◽  
R. Gill ◽  
J. Clevenger ◽  
P. Timper ◽  
C. C. Holbrook ◽  
...  
Keyword(s):  
Linkage Group ◽  
Diploid Species ◽  
Nematode Resistance ◽  
Distal Portion ◽  
Root Knot Nematode ◽  
Resistant Parent ◽  
Cultivated Peanut ◽  
Moderate Resistance ◽  
Wild Diploid Species ◽  
Introgressed Region

ABSTRACT Strong host resistance to root-knot nematode (RKN; Meloidogyne arenaria) introgressed from a wild diploid species to cultivated peanut was previously shown to be located on a large chromosomal region of linkage group A09. Little to no recombination in mapping populations has hindered fine mapping of the resistance genes. In order to further delineate the introgressed region, additional polymorphic markers were added to the linkage group A09 using a recombinant inbred line population developed from Gregory x Tifguard in which Gregory is the susceptible parent and Tifguard is the resistant parent harboring the alien introgression. Map distance within the introgressed region based on this population increased to 8 cM compared with zero recombination in an earlier generation. Lines with rare recombination within this introgressed region were phenotyped and it was demonstrated that one portion of the introgressed region confers moderate resistance while a smaller, distal portion confers strong resistance to RKN. Molecular markers associated with the introgressed region conferring strong resistance can be deployed in peanut breeding programs to improve selection for RKN resistance.

scholarly journals Morphological and reproductive characterization of nascent allotetraploids cross-compatible with cultivated peanut (Arachis hypogaea L.)

2021 ◽  
Author(s):  
Chandler Levinson ◽  
Ye Chu ◽  
Xuelin Luo ◽  
H. Thomas Stalker ◽  
Dongying Gao ◽  
...  
Keyword(s):  
Phenotypic Diversity ◽  
Phenotypic Variability ◽  
Diploid Species ◽  
Lower Percentage ◽  
Crop Breeding ◽  
Arachis Hypogaea L ◽  
Cultivated Peanut ◽  
Leaf Hairiness ◽  
Wild Diploid Species

AbstractPeanut improvement is limited by a narrow genetic base. However, this obstacle can be circumvented by incorporating phenotypic variability from wild, diploid Arachis species through interspecific hybridizations. In this study, four allotetraploid interspecific hybrids IpaCor4x (A. ipaensis × A. correntina), IpaDur4x (A. ipaensis × A. duranensis), IpaSten4x (A. ipaensis × A. stenosperma), and ValSten4x (A. valida × A. stenosperma) were created and morphologically characterized through the following parameters: flower count, flower size, flower banner pigmentation, leaf area and weight, leaf hairiness, main stem height, internode length, percent of reproductive nodes, biomass, 100 pod weight, and 100 seed weight. For every trait, except for flower banner absorption at 380 nm, at least one or more allotetraploids differed from the cultivated peanut control. In general, these allotetraploids had a greater production of flowers during the growing season, larger flowers, larger and hairier leaves, taller main stems, longer primary laterals, longer internodes, lower percentage of reproductive nodes, heavier plant body masses, and smaller seeds and pods. This phenotypic diversity can be utilized directly in ornamental and forage breeding, while for oil and food crop breeding, this diversity will likely need to be selected against while desirable traits such as disease and insect resistance and abiotic stress tolerances derived from the wild diploid species are maintained.

scholarly journals read_haps: using read haplotypes to detect same species contamination in DNA sequences

2020 ◽  
Author(s):  
Hannes P. Eggertsson ◽  
Bjarni V. Halldorsson
Keyword(s):  
Data Analysis ◽  
Genome Sequencing ◽  
Dna Sequences ◽  
Diploid Species ◽  
Reliable Data ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data ◽  
Short Read ◽  
Polymorphic Snps

AbstractMotivationData analysis is requisite on reliable data. In genetics this includes verifying that the sample is not contaminated with another, a problem ubiquitous in biology.ResultsIn human, and other diploid species, DNA contamination from the same species can be found by the presence of three haplotypes between polymorphic SNPs. read_haps is a tool that detects sample contamination from short read whole genome sequencing data.Availabilitygithub.com/DecodeGenetics/[email protected]

scholarly journals A genome sequence resource for the genus Passiflora , the genome of the wild diploid species Passiflora organensis

2021 ◽  
Author(s):  
Zirlane Portugal Costa ◽  
Alessandro Mello Varani ◽  
Luiz Augusto Cauz‐Santos ◽  
Mariela Analía Sader ◽  
Helena Augusto Giopatto ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Diploid Species ◽  
A Genome ◽  
Wild Diploid Species

scholarly journals The Gossypium anomalum genome as a resource for cotton improvement and evolutionary analysis of hybrid incompatibility

2021 ◽  
Author(s):  
Corrinne E. Grover ◽  
Daojun Yuan ◽  
Mark A. Arick ◽  
Emma R. Miller ◽  
Guanjing Hu ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Stress Resistance ◽  
De Novo ◽  
Diploid Species ◽  
Evolutionary Analysis ◽  
Hybrid Lethality ◽  
Genome Sequences ◽  
High Quality ◽  
Hybrid Incompatibility ◽  
Modern Breeding

Cotton is an important crop that has been the beneficiary of multiple genome sequencing efforts, including diverse representatives of wild species for germplasm development. Gossypium anomalum is a wild African diploid species that harbors stress-resistance and fiber-related traits with potential application to modern breeding efforts. In addition, this species is a natural source of cytoplasmic male sterility and a resource for understanding hybrid lethality in the genus. Here we report a high-quality de novo genome assembly for G. anomalum and characterize this genome relative to existing genome sequences in cotton. In addition, we use the synthetic allopolyploids 2(A2D1) and 2(A2D3) to discover regions in the G. anomalum genome potentially involved in hybrid lethality, a possibility enabled by introgression of regions homologous to the D3 (G. davidsonii) lethality loci into the synthetic 2(A2D3) allopolyploid.

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