Construction of genetic linkage map and identification of QTLs related to agronomic traits in maize using DNA transposon-based markers

This study reports a high density genetic linkage map based on the ‘Maryland 96-5722’ by ‘Spencer’ recombinant inbred line (RIL) population of soybean [Glycine max (L.) Merr.] and constructed exclusively with single nucleotide polymorphism (SNP) markers. The Illumina Infinium SoySNP6K BeadChip genotyping array produced 5,376 SNPs in the mapping population, with a 96.75% success rate. Significant level of goodness-of-fit for each locus was tested based on the observed vs. expected ratio (1:1). Out of 5,376 markers, 1,465 SNPs fit the 1:1 segregation rate having ≤20% missing data plus heterozygosity among the RILs. Among this 1,456 just 657 were polymorphic between the parents DNAs tested. These 657 SNPs were mapped using the JoinMap 4.0 software and 550 SNPs were distributed on 16 linkage groups (LGs) among the 20 chromosomes of the soybean genome. The total map length was just 201.57 centiMorgans (cM) with an average marker density of 0.37 cM. This is one of the high density SNP-based genetic linkage maps of soybean that will be used by the scientific community to map quantitative trait loci (QTL) and identify candidate genes for important agronomic traits in soybean.

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Construction of a high-density genetic linkage map and QTL mapping of oleic acid content and three agronomic traits in sunflower (Helianthus annuus L.) using specific-locus amplified fragment sequencing (SLAF-seq)

Breeding Science ◽

10.1270/jsbbs.18051 ◽

2018 ◽

Vol 68 (5) ◽

pp. 596-605 ◽

Cited By ~ 1

Author(s):

Fei Zhou ◽

Yan Liu ◽

Chunbo Liang ◽

Wenjun Wang ◽

Cen Li ◽

...

Keyword(s):

Oleic Acid ◽

Qtl Mapping ◽

Linkage Map ◽

Helianthus Annuus ◽

Acid Content ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Agronomic Traits ◽

Oleic Acid Content ◽

Specific Locus

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Development of Genetic Linkage Map and Identification of QTLs for Agronomic Traits in Chickpea (Cicer arietinum L.)

International Journal of Current Microbiology and Applied Sciences ◽

10.20546/ijcmas.2018.706.010 ◽

2018 ◽

Vol 7 (06) ◽

pp. 66-77

Author(s):

Dalpat Lal ◽

R.L. Ravikumar

Keyword(s):

Linkage Map ◽

Cicer Arietinum ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Agronomic Traits ◽

Cicer Arietinum L

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The development of a genetic linkage map of blackcurrant (Ribes nigrum L.) and the identification of regions associated with key fruit quality and agronomic traits

Euphytica ◽

10.1007/s10681-007-9412-8 ◽

2007 ◽

Vol 161 (1-2) ◽

pp. 19-34 ◽

Cited By ~ 29

Author(s):

Rex Brennan ◽

Linzi Jorgensen ◽

Christine Hackett ◽

Mary Woodhead ◽

Sandra Gordon ◽

...

Keyword(s):

Linkage Map ◽

Fruit Quality ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Agronomic Traits ◽

Ribes Nigrum

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Construction of a genetic linkage map and QTL mapping of agronomic traits in Auricularia auricula-judae

The Journal of Microbiology ◽

10.1007/s12275-017-7241-6 ◽

2017 ◽

Vol 55 (10) ◽

pp. 792-799 ◽

Cited By ~ 5

Author(s):

Li-Xin Lu ◽

Fang-Jie Yao ◽

Peng Wang ◽

Ming Fang ◽

You-Min Zhang ◽

...

Keyword(s):

Qtl Mapping ◽

Linkage Map ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Agronomic Traits ◽

Auricularia Auricula

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Genetic linkage and physical mapping for an oyster mushroom Pleurotus cornucopiae and QTL analysis for the trait cap color

Applied and Environmental Microbiology ◽

10.1128/aem.00953-21 ◽

2021 ◽

Author(s):

Yan Zhang ◽

Wei Gao ◽

Anton Sonnenberg ◽

Qiang Chen ◽

Jinxia Zhang ◽

...

Keyword(s):

Linkage Map ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

De Novo ◽

Agronomic Traits ◽

Snp Markers ◽

Biological Efficiency ◽

Solid Base ◽

Marker Assisted Breeding ◽

Oyster Mushrooms

Oyster mushrooms are grown commercially worldwide especially in many developing countries for their easy cultivation and high biological efficiency. Pleurotus cornucopiae is one of the main oyster mushrooms species for its gastronomic value and nutraceutical properties. Cap color is an important trait since consumers prefer dark colored mushrooms, which are now only represented by a small portion of the commercial varieties. Breeding efforts are greatly required to improve quality-related traits to satisfy various demands of consumers. Here we present a saturated genetic linkage map of P. cornucopiae constructed by using a segregating population of 122 monokaryons and 3449 SNP markers generated by 2b-RAD approach. The map contains 11 linkage groups covering 961.6 cM (centimorgan) with an average marker spacing of 0.27 cM. The genome of P. cornucopiae was de novo sequenced resulting in 425 scaffolds (>1000 bp) with a total genome size of 35.1 Mb. The scaffolds were assembled to pseudo-chromosome level with the assistance of the genetic linkage map. A total of 97% SNP markers (3357) were physically localized on 140 scaffolds that were assigned to 11 pseudo-chromosomes with a total of 32.5 Mb representing 92.5% of the whole genome. Six QTL controlling cap color of P. cornucopiae were detected explaining a total phenotypic variation of 65.6% with the highest value for the QTL on pseudo-chromosome 5 (18%). The results of our study provide a solid base for marker-assisted breeding for agronomic traits and especially for studies on biological mechanisms controlling cap color in oyster mushrooms. Importance Oyster mushrooms are produced and consumed over the world. Pleurotus cornucopiae is one of the main oyster mushrooms species. Dark cap oyster mushrooms are more and more popular to a consumer’s preferences, but dark varieties are rare to see on the market. Prerequisites for efficient breeding programs are the availability of high-quality whole genomes and genetic linkage maps. Genetic studies to fulfill some of these prerequisites have hardly been done for P. cornucopiae . In this study, we de novo sequenced the genome and constructed a saturated genetic linkage map for P. cornucopiae . The genetic linkage map was effectively used to assist the genome assembly and identify QTL that genetically control the trait cap color. Besides, the genome characteristics of P. cornucopiae was compared to its closely related species P . ostreatus . The results provided a basis for understanding the genetic background and marker-assisted breeding of this economic important mushroom species.

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