Genome-wide linkage mapping of yield-related traits in three Chinese bread wheat populations using high-density SNP markers

AbstractIt is predicted that high-temperature stress will increasingly affect crop yields worldwide as a result of climate change. In order to determine the genetic basis of thermotolerance of seed-set in maize under field conditions, we performed mapping of quantitative trait loci (QTLs) in a recombinant inbred line (RIL) population using a collection of 8329 specifically developed high-density single-nucleotide polymorphism (SNP) markers, combined with a genome-wide association study (GWAS) of 261 diverse maize lines using 259 973 SNPs. In total, four QTLs and 17 genes associated with 42 SNPs related to thermotolerance of seed-set were identified. Among them, four candidate genes were found in both linkage mapping and GWAS. Thermotolerance of seed-set was increased significantly in near-isogenic lines (NILs) that incorporated the four candidate genes in a susceptible parent background. The expression profiles of two of the four genes showed that they were induced by high temperatures in the maize tassel in a tolerant parent background. Our results indicate that thermotolerance of maize seed-set is regulated by multiple genes each of which has minor effects, with calcium signaling playing a central role. The genes identified may be exploited in breeding programs to improve seed-set and yield of maize under heat stress.

Download Full-text

Assessment of Genetic Differentiation and Linkage Disequilibrium in Solanum pimpinellifolium Using Genome-Wide High-Density SNP Markers

G3 Genes|Genome|Genetics ◽

10.1534/g3.118.200862 ◽

2019 ◽

Vol 9 (5) ◽

pp. 1497-1505 ◽

Cited By ~ 4

Author(s):

Ya-Ping Lin ◽

Chu-Yin Liu ◽

Kai-Yi Chen

Keyword(s):

Linkage Disequilibrium ◽

Genetic Differentiation ◽

Snp Markers ◽

High Density ◽

Solanum Pimpinellifolium ◽

Genome Wide

Download Full-text

Genome-wide Linkage Analysis with Clustered SNP Markers

CrossRef Listing of Deleted DOIs ◽

10.1177/1087057108327327 ◽

2008 ◽

Vol 14 (1) ◽

pp. 92-96 ◽

Cited By ~ 10

Author(s):

Kaja K. Selmer ◽

Kristin Brandal ◽

Ole K. Olstad ◽

Bård Birkenes ◽

Dag E. Undlien ◽

...

Keyword(s):

Linkage Analysis ◽

Linkage Mapping ◽

Snp Markers ◽

Monogenic Disease ◽

Comparison Of Methods ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Genome Wide ◽

A Genome ◽

Large Families

Single nucleotide polymorphisms (SNPs) have recently replaced microsatellites as the genetic markers of choice in linkage analysis, primarily because they are more abundant and the genotypes more amenable for automatic calling. One of the most recently launched linkage mapping sets (LMS) is the Applied Biosystems Human LMS 4K, which is a genome-wide linkage set based on the SNPlex™ technology and the use of clustered SNPs. In this article the authors report on their experience with this set and the associated genotyping software GeneMapper® version 4.0, which they have used for linkage analyses in 17 moderate to large families with assumed monogenic disease. For comparison of methods, they also performed a genome-wide linkage analysis in 1 of the 17 families using the Affymetrix GeneChip® Human Mapping 10K 2.0 array. The conclusion is that both methods performed technically well, with high call rates and comparable and low rates of Mendelian inconsistencies. However, genotyping is less automated in GeneMapper® version 4.0 than in the Affymetrix software and thus more time consuming. ( Journal of Biomolecular Screening 2009:92-96)

Download Full-text

Identification and QTL Analysis of Flavonoids and Carotenoids in Tetraploid Roses Based on an Ultra-High-Density Genetic Map

Frontiers in Plant Science ◽

10.3389/fpls.2021.682305 ◽

2021 ◽

Vol 12 ◽

Author(s):

Bixuan Cheng ◽

Huihua Wan ◽

Yu Han ◽

Chao Yu ◽

Le Luo ◽

...

Keyword(s):

Qtl Analysis ◽

Average Distance ◽

Flower Color ◽

Snp Markers ◽

High Density ◽

Linkage Groups ◽

Genome Wide ◽

Final Length ◽

Ssr And Snp Markers ◽

Whole Genome Resequencing

Roses are highly valuable within the flower industry. The metabolites of anthocyanins, flavonols, and carotenoids in rose petals are not only responsible for the various visible petal colors but also important bioactive compounds that are important for human health. In this study, we performed a QTL analysis on pigment contents to locate major loci that determine the flower color traits. An F1 population of tetraploid roses segregating for flower color was used to construct an ultra-high-density genetic linkage map using whole-genome resequencing technology to detect genome-wide SNPs. Previously developed SSR and SNP markers were also utilized to increase the marker density. Thus, a total of 9,259 markers were mapped onto seven linkage groups (LGs). The final length of the integrated map was 1285.11 cM, with an average distance of 0.14 cM between adjacent markers. The contents of anthocyanins, flavonols and carotenoids of the population were assayed to enable QTL analysis. Across the 33 components, 46 QTLs were detected, explaining 11.85–47.72% of the phenotypic variation. The mapped QTLs were physically clustered and primarily distributed on four linkage groups, namely LG2, LG4, LG6, and LG7. These results improve the basis for flower color marker-assisted breeding of tetraploid roses and guide the development of rose products.

Download Full-text