scholarly journals High density linkage mapping of genomic and transcriptomic SNPs for synteny analysis and anchoring the genome sequence of chickpea

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Rashmi Gaur ◽  
Ganga Jeena ◽  
Niraj Shah ◽  
Shefali Gupta ◽  
Seema Pradhan ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Linkage Mapping ◽  
High Density ◽  
Synteny Analysis

High-density linkage mapping for agronomic and physiological traits of rice (Oryza sativa L.) under reproductive-stage salt stress

2021 ◽  
Vol 100 (2) ◽  
Author(s):  
Mostafa Ahmadizadeh ◽  
Nadali Babaeian-Jelodar ◽  
Ghasem Mohammadi-Nejad ◽  
Nadali Bagheri ◽  
Rakesh Kumar Singh
Keyword(s):  
Oryza Sativa ◽  
Salt Stress ◽  
Linkage Mapping ◽  
Oryza Sativa L ◽  
High Density ◽  
Reproductive Stage ◽  
Physiological Traits

Drought response QTLs in a Super Basmati × Azucena population by high‐density GBS‐based SNP linkage mapping

2021 ◽  
Author(s):  
Raheela Waheed ◽  
John Carlos Ignacio ◽  
Juan David Arbelaez ◽  
Venice Margarette Juanillas ◽  
Muhammad Asif ◽  
...  
Keyword(s):  
Linkage Mapping ◽  
High Density ◽  
Drought Response

scholarly journals QTL Mapping of Fruit and Seed-related Traits in Watermelon Using Genotyping-by-Sequencing-based High-density Linkage Mapping

2020 ◽  
Author(s):  
Meiling Gao ◽  
Xiaoxue Liang ◽  
Xiujie Liu ◽  
Yu Guo ◽  
Hongguo Xu ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Seed Size ◽  
Fruit Quality ◽  
Linkage Mapping ◽  
Genotyping By Sequencing ◽  
Fruit Shape ◽  
High Density ◽  
Chromosome 2 ◽  
Phenotypic Data ◽  
Stripe Pattern

Abstract BackgroundWatermelon is an important vegetable crop with dual use of both fruit and seeds. Understanding the genetic basis of fruit quality and seed size-related traits is important for efficient marker-assisted breeding in watermelon. Linkage mapping in watermelon segregating populations using genotyping-by-sequencing (GBS) provides insights into genetic control of fruit- and seed-related traits and genome collinearity in commercial watermelon cultivars. ResultsIn the present study, we conducted QTL mapping of 12 horticulturally important traits on external and internal fruit quality and seed size/weight using segregating populations derived a cross between two commercial varieties. A high-density genetic map was developed with GBS which contained more than 6,000 SNP loci in 1,004 bins with a total map length of 1261.1 cM and average marker interval of 1.26 cM or 329 kb. Phenotypic data of fruit rind color (RC), rind stripe pattern (RSP), flesh color (FFC), fruit diameter (FD), fruit length (FL), fruit shape index (FSI), fruit weight (FW), Brix content central (BCC), Brix content edge (BCE), seed length (SL), width (SW), and weight (20SWT) were collected from two locations in two years. QTL analysis identified 47 QTL for the 12 traits, of which 24 had moderate- or major-effects, and 34 were novel QTL not identified in previous studies. The QTL for RSP were identified overlapped with previous reports, and mapped the QTL to a small interval on chromosome 6. From the detected novel QTL, we identify FD (qfd2.1), FL (qfl2.1) co-located with FSI (qfsi2.1) QTL on chromosome 2, and the minor QTL qfw3.2 co-located with previously reported fruit shape QTL (qfd3.1, qfl3.1, qfsi3.1), and SW (qsw10.1) co-located with 20SWT QTL (q20swt10.1) on chromosome 10, and 5 minor QTL (qbcc2.1, qbcc5.1, qbce2.1, qbce2.2, qbce5.1) were found to be likely new locus for Brix content.ConclusionWe conducted GBS consisting of 120 F2 individuals and developed a high-density linkage map with more than 6,000 SNP loci in 1004 bins in watermelon. We identified 47 QTL for 12 fruit and seed related traits including 34 novel QTL. Our work expands the molecular breeding toolbox for watermelon to improve the yield and fruit quality.

scholarly journals Exploiting genotyping by sequencing to characterize the genomic structure of the American cranberry through high-density linkage mapping

BMC Genomics ◽  
2016 ◽  
Vol 17 (1) ◽  
Author(s):  
Giovanny Covarrubias-Pazaran ◽  
Luis Diaz-Garcia ◽  
Brandon Schlautman ◽  
Joseph Deutsch ◽  
Walter Salazar ◽  
...  
Keyword(s):  
Linkage Mapping ◽  
Genomic Structure ◽  
Genotyping By Sequencing ◽  
High Density ◽  
American Cranberry

scholarly journals Significance testing and genomic inflation factor using high‐density genotypes or whole‐genome sequence data

2019 ◽  
Vol 136 (6) ◽  
pp. 418-429 ◽  
Author(s):  
Sanne den Berg ◽  
Jérémie Vandenplas ◽  
Fred A. Eeuwijk ◽  
Marcos S. Lopes ◽  
Roel F. Veerkamp
Keyword(s):  
Genome Sequence ◽  
Sequence Data ◽  
High Density ◽  
Whole Genome Sequence ◽  
Significance Testing ◽  
Whole Genome ◽  
Genome Sequence Data ◽  
Inflation Factor
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