scholarly journals A High‐Density Linkage Map of the Ancestral Diploid Strawberry, Fragaria iinumae , Constructed with Single Nucleotide Polymorphism Markers from the IStraw90 Array and Genotyping by Sequencing

2016 ◽  
Vol 9 (2) ◽  
Author(s):  
Lise L. Mahoney ◽  
Daniel J. Sargent ◽  
F. Abebe‐Akele ◽  
Dave J. Wood ◽  
Judson A. Ward ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Linkage Map ◽  
Genotyping By Sequencing ◽  
High Density ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
High Density Linkage Map ◽  
Diploid Strawberry

scholarly journals High‐Density Single Nucleotide Polymorphism Linkage Maps of Lowland Switchgrass using Genotyping‐by‐Sequencing

2015 ◽  
Vol 8 (2) ◽  
Author(s):  
Jason D. Fiedler ◽  
Christina Lanzatella ◽  
Miki Okada ◽  
Jerry Jenkins ◽  
Jeremy Schmutz ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Genotyping By Sequencing ◽  
High Density ◽  
Linkage Maps ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide

scholarly journals Genetic Diversity of Purple Passion Fruit, Passiflora edulis f. edulis, Based on Single-Nucleotide Polymorphism Markers Discovered through Genotyping by Sequencing

Diversity ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 144
Author(s):  
Nohra Castillo Rodríguez ◽  
Xingbo Wu ◽  
María Isabel Chacón ◽  
Luz Marina Melgarejo ◽  
Matthew Wohlgemuth Blair
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphism ◽  
Genotyping By Sequencing ◽  
Passion Fruit ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Passiflora Edulis ◽  
Tropical Fruit ◽  
Commercial Cultivars ◽  
Purple Passion Fruit

Orphan crops, which include many of the tropical fruit species used in the juice industry, lack genomic resources and breeding efforts. Typical of this dilemma is the lack of commercial cultivars of purple passion fruit, Passiflora edulis f. edulis, and of information on the genetic resources of its substantial semiwild gene pool. In this study, we develop single-nucleotide polymorphism (SNP) markers for the species and show that the genetic diversity of this fruit crop has been reduced because of selection for cultivated genotypes compared to the semiwild landraces in its center of diversity. A specific objective of the present study was to determine the genetic diversity of cultivars, genebank accession, and landraces through genotyping by sequencing (GBS) and to conduct molecular evaluation of a broad collection for the species P. edulis from a source country, Colombia. We included control genotypes of yellow passion fruit, P. edulis f. flavicarpa. The goal was to evaluate differences between fruit types and compare landraces and genebank accessions from in situ accessions collected from farmers. In total, 3820 SNPs were identified as informative for this diversity study. However, the majority distinguished yellow and purple passion fruit, with 966 SNPs useful in purple passion fruits alone. In the population structure analysis, purple passion fruits were very distinct from the yellow ones. The results for purple passion fruits alone showed reduced diversity for the commercial cultivars while highlighting the higher diversity found among landraces from wild or semi-wild conditions. These landraces had higher heterozygosity, polymorphism, and overall genetic diversity. The implications for genetics and breeding as well as evolution and ecology of purple passion fruits based on the extant landrace diversity are discussed with consideration of manual or pollinator-assisted hybridization of this species.

RAD-seq-Based High-Density Linkage Map Construction and QTL Mapping of Biomass-Related Traits in Sorghum using the Japanese Landrace Takakibi NOG

2020 ◽  
Vol 61 (7) ◽  
pp. 1262-1272
Author(s):  
Hiromi Kajiya-Kanegae ◽  
Hideki Takanashi ◽  
Masaru Fujimoto ◽  
Motoyuki Ishimori ◽  
Norikazu Ohnishi ◽  
...  
Keyword(s):  
Linkage Map ◽  
High Density ◽  
Genomic Diversity ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genetic Traits ◽  
Map Construction ◽  
Days To Heading ◽  
High Density Linkage Map ◽  
Sorghum Bicolor L

Abstract Sorghum [Sorghum bicolor (L.) Moench] grown locally by Japanese farmers is generically termed Takakibi, although its genetic diversity compared with geographically distant varieties or even within Takakibi lines remains unclear. To explore the genomic diversity and genetic traits controlling biomass and other physiological traits in Takakibi, we focused on a landrace, NOG, in this study. Admixture analysis of 460 sorghum accessions revealed that NOG belonged to the subgroup that represented Asian sorghums, and it was only distantly related to American/African accessions including BTx623. In an attempt to dissect major traits related to biomass, we generated a recombinant inbred line (RIL) from a cross between BTx623 and NOG, and we constructed a high-density linkage map based on 3,710 single-nucleotide polymorphisms obtained by restriction-site-associated DNA sequencing of 213 RIL individuals. Consequently, 13 fine quantitative trait loci (QTLs) were detected on chromosomes 2, 3, 6, 7, 8 and 9, which included five QTLs for days to heading, three for plant height (PH) and total shoot fresh weight and two for Brix. Furthermore, we identified two dominant loci for PH as being identical to the previously reported dw1 and dw3. Together, these results corroborate the diversified genome of Japanese Takakibi, while the RIL population and high-density linkage map generated in this study will be useful for dissecting other important traits in sorghum.

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