scholarly journals Preliminary Genetic Map of a New Recombinant Inbred Line Population for Narrow-leafed Lupin (Lupinus angustifolius L.)

Agronomy ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 653 ◽  
Author(s):  
Bartosz Kozak ◽  
Renata Galek ◽  
Dariusz Zalewski ◽  
Ewa Sawicka-Sienkiewicz
Keyword(s):  
Genetic Map ◽  
Genome Wide Association Study ◽  
Reference Genome ◽  
High Density ◽  
Genetic Maps ◽  
New Variety ◽  
Model Legume ◽  
Speed Up ◽  
Trait Locus ◽  
Next Generation Sequencing Ngs

Genetic maps are an essential tool for investigating molecular markers’ linkage with traits of agronomic importance. Breeders put a lot of emphasis on this type of markers, which are used in breeding programs implementation and speed up the process of a new variety development. In this paper, we construct a new, high-density linkage genetic map for Polish material on narrow-leafed lupin. The mapping population originated from crossing the Polish variety ‘Emir’ and the Belarusian breeding line ‘LAE-1’. A new map was constructed based on DArTseq markers—a new type of marker generated with the next-generation sequencing (NGS) technique. The map was built with 4602 markers, which are divided into 20 linkage groups, corresponding with the number of gametic chromosomes in narrow-leafed lupin. On the new map there are 1174 unique loci. The total length of all linkage group is 3042 cM. This map was compared to the reference genome of narrow-leafed lupin and the CDS sequence for model legume species: emphMedicago truncatula, emphLotus japonicus and Glycine max. Analysis revealed the presence of the DArTseq marker common for all investigated species. We were able to map 38 new, unplaced scaffolds on the new genetic map of narrow-leafed lupin. The high-density genetic map we received can be used for quantitative trait locus (QTL) mapping, genome-wide association study analysis and assembly of the reference genome for the whole genome sequencing (WGS) method

scholarly journals Identification of QTLs for Stripe Rust Resistance in a Recombinant Inbred Line Population

2019 ◽  
Vol 20 (14) ◽  
pp. 3410 ◽  
Author(s):  
Manyu Yang ◽  
Guangrong Li ◽  
Hongshen Wan ◽  
Liping Li ◽  
Jun Li ◽  
...  
Keyword(s):  
Genetic Map ◽  
Stripe Rust ◽  
Resistance Genes ◽  
Phenotypic Variation ◽  
Recombinant Inbred ◽  
Rust Resistance ◽  
High Density ◽  
Genetic Maps ◽  
Stripe Rust Resistance ◽  
Resistance Locus

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most devastating fungal diseases of wheat worldwide. It is essential to discover more sources of stripe rust resistance genes for wheat breeding programs. Specific locus amplified fragment sequencing (SLAF-seq) is a powerful tool for the construction of high-density genetic maps. In this study, a set of 200 recombinant inbred lines (RILs) derived from a cross between wheat cultivars Chuanmai 42 (CH42) and Chuanmai 55 (CH55) was used to construct a high-density genetic map and to identify quantitative trait loci (QTLs) for stripe rust resistance using SLAF-seq technology. A genetic map of 2828.51 cM, including 21 linkage groups, contained 6732 single nucleotide polymorphism markers (SNP). Resistance QTLs were identified on chromosomes 1B, 2A, and 7B; Qyr.saas-7B was derived from CH42, whereas Qyr.saas-1B and Qyr.saas-2A were from CH55. The physical location of Qyr.saas-1B, which explained 6.24–34.22% of the phenotypic variation, overlapped with the resistance gene Yr29. Qyr.saas-7B accounted for up to 20.64% of the phenotypic variation. Qyr.saas-2A, a minor QTL, was found to be a likely new stripe rust resistance locus. A significant additive effect was observed when all three QTLs were combined. The combined resistance genes could be of value in breeding wheat for stripe rust resistance.

scholarly journals Construction of a high-resolution genetic map and identification of quantitative trait loci for salt tolerance in jute (Corchous spp.)

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Zemao Yang ◽  
Youxin Yang ◽  
Zhigang Dai ◽  
Dongwei Xie ◽  
Qing Tang ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Qtl Mapping ◽  
Genetic Map ◽  
Quantitative Trait ◽  
High Density ◽  
Genetic Maps ◽  
Interval Length ◽  
Phenotypic Variance ◽  
Qtls Mapping

Abstract Background Jute (Corchorus spp.) is the most important natural fiber crop after cotton in terms of cultivation area and production. Salt stress greatly restricts plant development and growth. A high-density genetic linkage map is the basis of quantitative trait locus (QTLs) mapping. Several high-density genetic maps and QTLs mapping related to salt tolerance have been developed through next-generation sequencing in many crop species. However, such studies are rare for jute. Only several low-density genetic maps have been constructed and no salt tolerance-related QTL has been mapped in jute to date. Results We developed a high-density genetic map with 4839 single nucleotide polymorphism markers spanning 1375.41 cM and an average distance of 0.28 cM between adjacent markers on seven linkage groups (LGs) using an F2 jute population, LGs ranged from LG2 with 299 markers spanning 113.66 cM to LG7 with 1542 markers spanning 350.18 cM. In addition, 99.57% of gaps between adjacent markers were less than 5 cM. Three obvious and 13 minor QTLs involved in salt tolerance were identified on four LGs explaining 0.58–19.61% of the phenotypic variance. The interval length of QTL mapping varied from 1.3 to 20.2 cM. The major QTL, qJST-1, was detected under two salt stress conditions that explained 11.81 and 19.61% of the phenotypic variation, respectively, and peaked at 19.3 cM on LG4. Conclusions We developed the first high-density and the most complete genetic map of jute to date using a genotyping-by-sequencing approach. The first QTL mapping related to salt tolerance was also carried out in jute. These results should provide useful resources for marker-assisted selection and transgenic breeding for salt tolerance at the germination stage in jute.

scholarly journals Quantitative Trait Locus (QTLs) Mapping for Quality Traits of Wheat Based on High Density Genetic Map Combined With Bulked Segregant Analysis RNA-seq (BSR-Seq) Indicates That the Basic 7S Globulin Gene Is Related to Falling Number

2020 ◽  
Vol 11 ◽  
Author(s):  
Qiao Li ◽  
Zhifen Pan ◽  
Yuan Gao ◽  
Tao Li ◽  
Junjun Liang ◽  
...  
Keyword(s):  
Genetic Map ◽  
Quantitative Trait ◽  
Recombinant Inbred Lines ◽  
High Density ◽  
Genetic Maps ◽  
Phenotypic Variance ◽  
Quality Traits ◽  
Rna Seq ◽  
Falling Number ◽  
7S Globulin

Numerous quantitative trait loci (QTLs) have been identified for wheat quality; however, most are confined to low-density genetic maps. In this study, based on specific-locus amplified fragment sequencing (SLAF-seq), a high-density genetic map was constructed with 193 recombinant inbred lines derived from Chuanmai 42 and Chuanmai 39. In total, 30 QTLs with phenotypic variance explained (PVE) up to 47.99% were identified for falling number (FN), grain protein content (GPC), grain hardness (GH), and starch pasting properties across three environments. Five NAM genes closely adjacent to QGPC.cib-4A probably have effects on GPC. QGH.cib-5D was the only one detected for GH with high PVE of 33.31–47.99% across the three environments and was assumed to be related to the nearest pina-D1 and pinb-D1genes. Three QTLs were identified for FN in at least two environments, of which QFN.cib-3D had relatively higher PVE of 16.58–25.74%. The positive effect of QFN.cib-3D for high FN was verified in a double-haploid population derived from Chuanmai 42 × Kechengmai 4. The combination of these QTLs has a considerable effect on increasing FN. The transcript levels of Basic 7S globulin and Basic 7S globulin 2 in QFN.cib-3D were significantly different between low FN and high FN bulks, as observed through bulk segregant RNA-seq (BSR). These QTLs and candidate genes based on the high-density genetic map would be beneficial for further understanding of the genetic mechanism of quality traits and molecular breeding of wheat.

scholarly journals A High-Density Genetic Map with Array-Based Markers Facilitates Structural and Quantitative Trait Locus Analyses of the Common Wheat Genome

DNA Research ◽  
2014 ◽  
Vol 21 (5) ◽  
pp. 555-567 ◽  
Author(s):  
Julio Cesar Masaru Iehisa ◽  
Ryoko Ohno ◽  
Tatsuro Kimura ◽  
Hiroyuki Enoki ◽  
Satoru Nishimura ◽  
...  
Keyword(s):  
Quantitative Trait Locus ◽  
Common Wheat ◽  
Genetic Map ◽  
Quantitative Trait ◽  
High Density ◽  
Wheat Genome ◽  
The Common ◽  
Trait Locus

scholarly journals Identify of Fast-Growing Related Genes Especially in Height Growth by Combining QTL Analysis and Transcriptome in Salix matsudana (Koidz)

2021 ◽  
Vol 12 ◽  
Author(s):  
Guoyuan Liu ◽  
Qingshan Yang ◽  
Junfeng Gao ◽  
Yuwei Wu ◽  
Zhicong Feng ◽  
...  
Keyword(s):  
Genetic Map ◽  
Genetic Regulation ◽  
Lignin Biosynthesis ◽  
Principal Component ◽  
Height Growth ◽  
High Density ◽  
Genetic Maps ◽  
Pcr Analysis ◽  
Total Size ◽  
Fast Growing

The study on the fast-growing traits of trees, mainly valued by tree height (TH) and diameter at breast height (DBH), is of great significance to promote the development of the forest industry. Quantitative trait locus (QTL) mapping based on high-density genetic maps is an efficient approach to identify genetic regions for fast-growing traits. In our study, a high-density genetic map for the F1 population was constructed. The genetic map had a total size of 5,484.07 centimorgan (cM), containing 5,956 single nucleotide polymorphisms (SNPs) based on Specific Length Amplified Fragment sequencing. Six fast-growing related stable QTL were identified on six chromosomes, and five stable QTL were identified by a principal component analysis (PCA). By combining the RNA-seq analysis for the two parents and two progenies with the qRT-PCR analysis, four candidate genes, annotated as DnaJ, 1-aminocyclopropane-1-carboxylate oxidase 1 (ACO1), Caffeic acid 3-O-methyltransferase 1 (COMT1), and Dirigent protein 6 (DIR6), that may regulate height growth were identified. Several lignin biosynthesis-related genes that may take part in height growth were detected. In addition, 21 hotspots in this population were found. The results of this study will provide an important foundation for further studies on the molecular and genetic regulation of TH and DBH.

scholarly journals Molecular Characterisation of a Supergene Conditioning Super-High Vitamin C in Kiwifruit Hybrids

Plants ◽  
2019 ◽  
Vol 8 (7) ◽  
pp. 237
Author(s):  
John McCallum ◽  
William Laing ◽  
Sean Bulley ◽  
Susan Thomson ◽  
Andrew Catanach ◽  
...  
Keyword(s):  
Vitamin C ◽  
Genome Wide Association Study ◽  
Major Gene ◽  
Genetic Maps ◽  
Molecular Fingerprint ◽  
Pcr Marker ◽  
High Vitamin ◽  
Single Quantitative Trait Locus ◽  
Gene Segregation ◽  
Trait Locus

During analysis of kiwifruit derived from hybrids between the high vitamin C (ascorbic acid; AsA) species Actinidia eriantha and A. chinensis, we observed bimodal segregation of fruit AsA concentration suggesting major gene segregation. To test this hypothesis, we performed whole-genome sequencing on pools of hybrid genotypes with either high or low AsA fruit. Pool-GWAS (genome-wide association study) revealed a single Quantitative Trait Locus (QTL) spanning more than 5 Mbp on chromosome 26, which we denote as qAsA26.1. A co-dominant PCR marker was used to validate this association in four diploid (A. chinensis × A. eriantha) × A. chinensis backcross families, showing that the A. eriantha allele at this locus increases fruit AsA levels by 250 mg/100 g fresh weight. Inspection of genome composition and recombination in other A. chinensis genetic maps confirmed that the qAsA26.1 region bears hallmarks of suppressed recombination. The molecular fingerprint of this locus was examined in leaves of backcross validation families by RNA sequencing (RNASEQ). This confirmed strong allelic expression bias across this region as well as differential expression of transcripts on other chromosomes. This evidence suggests that the region harbouring qAsA26.1 constitutes a supergene, which may condition multiple pleiotropic effects on metabolism.

scholarly journals Segregation Distortion for Male Parents in High Density Genetic Maps from Reciprocal Crosses between Two Self-Incompatible Cultivars Confirms a Gametophytic System for Self-Incompatibility in Citrus

Agriculture ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 379
Author(s):  
Patrick Ollitrault ◽  
Dalel Ahmed ◽  
Gilles Costantino ◽  
Jean-Charles Evrard ◽  
Celine Cardi ◽  
...  
Keyword(s):  
Segregation Distortion ◽  
Molecular Mechanisms ◽  
Reference Genome ◽  
High Density ◽  
Genetic Maps ◽  
Chromosome 7 ◽  
Self Incompatibility ◽  
S Locus ◽  
Reciprocal Crosses ◽  
Seedless Fruits

Self-incompatibility is an important evolutionary feature in angiosperms and has major implications for breeding strategies in horticultural crops. In citrus, when coupled with parthenocarpy, it enables the production of seedless fruits in a mono-varietal orchard. A gametophytic incompatibility system with one S locus was proposed for citrus, but its molecular mechanisms remain the subject of debate. The objective of this work was to locate the S locus by the analyzing segregation distortion in reciprocal crosses of two self-incompatible citrus sharing one self-incompatible allele and to compare this location with previously published models. High density genetic maps of ‘Fortune’ mandarin and ‘Ellendale tangor’ with, respectively, 2164 SNP and 1467 SNP markers, were constructed using genotyping by sequencing data. They are highly syntenic and collinear with the clementine genome. Complete rejection of one allele was only observed in male segregation in the two parents and in only one genomic area, at the beginning of chromosome 7 of the clementine reference genome. Haplotype data in the area surrounding the theoretical S locus were in agreement with previously proposed S genotypes. Overall, our results are in full agreement with the recently proposed gametophytic S-RNase system with the S locus at the beginning of chromosome 7 of the clementine reference genome.

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