scholarly journals A Genotyping-by-sequencing Single Nucleotide Polymorphism–based Map and Genetic Analysis of Root Traits in an Interspecific Tomato Population

2019 ◽  
Vol 144 (6) ◽  
pp. 394-404 ◽  
Author(s):  
Limeng Xie ◽  
Patricia Klein ◽  
Kevin Crosby ◽  
John Jifon
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Root Length ◽  
Specific Root Length ◽  
Genotyping By Sequencing ◽  
Root Traits ◽  
Root Mass ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Shoot Mass ◽  
Root And Shoot Traits

Roots impact plants’ capacity to absorb water and nutrients and thus play a vital role in tolerance to drought, salinity, and nutrient stress. In tomato (Solanum lycopersicum) breeding programs, wild tomato species have been commonly used to increase disease resistance and fruit quality and yield. However, tomato has seldom been bred for water/nutrient use efficiency or resilience to abiotic stress. Meanwhile, little knowledge of the genetic control of root traits in tomato is available. In this study, a mapping population consisting of 181 F2 progenies derived from a cross between an advanced breeding line RvT1 (S. lycopersicum) and a wild species Lche4 (Solanum cheesmaniae) was evaluated for root and shoot traits in the greenhouse. Root phenotypes were studied for the early seedling stage. Heritability estimates show that root traits are moderately or highly heritable. Root mass was highly correlated with root size (length, surface area, and volume). Shoot mass and chlorophyll content (SPAD) were moderately correlated with root mass and size. Genotyping-by-sequencing was applied to discover single nucleotide polymorphism (SNP) markers. Seven hundred and forty-two SNPs were successfully mapped, and a medium-dense linkage map was created that covered 1319.47 centimorgans (cM) with an average distance of 1.78 cM between adjacent markers. Using composite interval mapping, multiple quantitative trait loci (QTL) mapping and nonparametric mapping, 29 QTLs were identified for 12 root and shoot traits on eight chromosomes. Those QTLs of major and minor effect were involved in the differences among the F2 population. Two QTL hotspot regions associated with root mass, size, shoot mass and SPAD were identified on chromosomes 1 and 4, which was consistent with the correlation among traits. Five QTLs for shoot length and eight QTLs for SPAD were accounting for 40.01% and 55.53% of the phenotypic variation. Two QTLs were associated with 18.26% of the total variation for specific root length. The wild parent Lche4 has been characterized as a potential genetic donor of higher specific root length and might be a good parent to modify the root system of cultivated tomato.

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.

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 Suitability of Single-Nucleotide Polymorphism Arrays Versus Genotyping-By-Sequencing for Genebank Genomics in Wheat

2020 ◽  
Vol 11 ◽  
Author(s):  
Jianting Chu ◽  
Yusheng Zhao ◽  
Sebastian Beier ◽  
Albert W. Schulthess ◽  
Nils Stein ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Genotyping By Sequencing ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide

scholarly journals Applying targeted genotyping by sequencing with a new set of nuclear and plastid SNP and indel loci for Quercus robur and Quercus petraea

2021 ◽  
Author(s):  
Bernd Degen ◽  
Celine Blanc-Jolivet ◽  
Svetlana Bakhtina ◽  
Ruslan Ianbaev ◽  
Yulai Yanbaev ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Quercus Robur ◽  
Restriction Site ◽  
Sequence Data ◽  
Genotyping By Sequencing ◽  
Quercus Petraea ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Genetic Studies ◽  
Genotyping Platform

AbstractWe used Double Digest Restriction site associated DNA sequencing (ddRAD) and Miseq to develop new geographically informative nuclear and plastid SNP and indel loci in Quercus robur and Q. petraea. Genotypes derived from sequence data of 95 individuals and two pools of 20 individuals each of Q. robur and Q. mongolica covering the distribution range of the species, were analysed to select geographically informative and polymorphic loci within Germany and Russia. We successfully screened a selected set of 431 nuclear single nucleotide polymorphism (nSNP), six nuclear Indel, six mitochondrial single nucleotide polymorphism (mtSNP) and ten chloroplast single nucleotide polymorphism (cpSNP) loci with a SeqSNP genotyping platform on 100 individuals Quercus petraea from 10 locations in Germany, 100 individuals Quercus robur from ten locations in Germany and 100 individuals Quercus robur from ten locations in Russia. The newly developed loci are useful for species identification and genetic studies on the genetic diversity and genetic differentiation of Quercus robur and Quercus petraea in Europe.

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