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 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 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 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 Construction of a High-density Genetic Map and Identification of Candidate Genes for Resistance to Fusarium Wilt based on the Resequencing of Recombinant Inbred Line Population in Gossypium Barbadense

2021 ◽  
Author(s):  
Wanli Han ◽  
Jieyin Zhao ◽  
Xiaojuan Deng ◽  
Aixing Gu ◽  
Duolu Li ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Genetic Map ◽  
Fusarium Wilt ◽  
Recombinant Inbred ◽  
Gene Annotation ◽  
Recombinant Inbred Lines ◽  
Fiber Quality ◽  
Gossypium Barbadense ◽  
High Density ◽  
Pcr Analysis

Abstract Background: Resistance to Fusarium wilt (FW) is of great significance for increasing the yield of Gossypium barbadense. Most published genetic studies on G. barbadense focus on yield and fiber quality traits, while there are few reports on resistance to FW. Results: To understand the genetic basis of cotton resistance to FW, this study used 110 recombinant inbred lines (RILs) of G. barbadense obtained from the parental materials Xinhai 14 and 06-146, and Nannong was used to construct a high-density genetic linkage map. The high-density genetic map was based on the resequencing of 933,845 single-nucleotide polymorphism (SNP) markers, and 3627 bins covering 2483.17 cM were finally obtained. The collinearity matched the physical map. A total of 9 QTLs for FW resistance were identified, each QTL explained 4.27-14.92% of the observed phenotypic variation, and qFW-Dt3-1 was identified in at least two environments. According to gene annotation information from multiple databases, promoter homeopathic elements and transcriptome data, 10 candidate genes were screened in a stable QTL interval. qRT-PCR analysis showed that the GOBAR_DD06292 gene was differentially expressed in the roots of the two parents under FW stress and exhibited the same expression trend in the G. barbadense resource materials.Conclusions: These results indicate the importance of the GOBAR_DD06292 gene in FW resistance in G. barbadense and lay a molecular foundation for the analysis of the molecular mechanism of FW in G. barbadense.

scholarly journals Restriction site-associated DNA sequencing for SNP discovery and high-density genetic map construction in southern catfish ( Silurus meridionalis )

2018 ◽  
Vol 5 (5) ◽  
pp. 172054 ◽  
Author(s):  
Mimi Xie ◽  
Yao Ming ◽  
Feng Shao ◽  
Jianbo Jian ◽  
Yaoguang Zhang ◽  
...  
Keyword(s):  
Linkage Map ◽  
Genetic Map ◽  
Restriction Site ◽  
Genome Structure ◽  
High Density ◽  
Genetic Maps ◽  
High Quality ◽  
Silurus Meridionalis ◽  
Map Construction ◽  
High Density Linkage Map

Single-nucleotide polymorphism (SNP) markers and high-density genetic maps are important resources for marker-assisted selection, mapping of quantitative trait loci (QTLs) and genome structure analysis. Although linkage maps in certain catfish species have been obtained, high-density maps remain unavailable in the economically important southern catfish ( Silurus meridionalis ). Recently developed restriction site-associated DNA (RAD) markers have proved to be a promising tool for SNP detection and genetic map construction. The objective of the present study was to construct a high-density linkage map using SNPs generated by next-generation RAD sequencing in S. meridionalis for future genetic and genomic studies. An F1 population of 100 individuals was obtained by intraspecific crossing of two wild heterozygous individuals. In total, 77 634 putative high-quality bi-allelic SNPs between the parents were discovered by mapping the parents' paired-end RAD reads onto the reference contigs from both parents, of which 54.7% were transitions and 45.3% were transversions (transition/transversion ratio of 1.2). Finally, 26 714 high-quality RAD markers were grouped into 29 linkage groups by using de novo clustering methods (Stacks). Among these markers, 4514 were linked to the female genetic map, 23 718 to the male map and 6715 effective loci were linked to the integrated map spanning 5918.31 centimorgans (cM), with an average marker interval of 0.89 cM. High-resolution genetic maps are a useful tool for both marker-assisted breeding and various genome investigations in catfish, such as sequence assembly, gene localization, QTL detection and genome structure comparison. Hence, such a high-density linkage map will serve as a valuable resource for comparative genomics and fine-scale QTL mapping in catfish species.

scholarly journals Identification and High-Density Mapping of Gene-Rich Regions in Chromosome Group 1 of Wheat

Genetics ◽  
1996 ◽  
Vol 144 (4) ◽  
pp. 1883-1891 ◽  
Author(s):  
Kulvinder S Gill ◽  
Bikram S Gill ◽  
Takashi R Endo ◽  
Teri Taylor
Keyword(s):  
Genetic Map ◽  
Physical Map ◽  
Average Distance ◽  
High Density ◽  
Genetic Maps ◽  
Cdna Clones ◽  
Density Mapping ◽  
Physical Maps ◽  
Group 1 Chromosomes ◽  
Group 1

We studied the distribution of genes and recombination in wheat (Triticum aestivum) group 1 chromosomes by comparing high-density physical and genetic maps. Physical maps of chromosomes 1A, 1B, and 1D were generated by mapping 50 DNA markers on 56 single-break deletion lines. A consensus physical map was compared with the 1D genetic map of Triticum tauschii (68 markers) and a Triticeae group 1 consensus map (288 markers) to generate a cytogenetic ladder map (CLM). Most group 1 markers (86%) were present in five clusters that encompassed only 10% of the group 1 chromosome. This distribution may reflect that of genes because more than half of the probes were cDNA clones and 30% were PstI genomic. All 14 agronomically important genes in group 1 chromosomes were present in these clusters. Most recombination occurred in gene-cluster regions. Markers fell at an average distance of 244 kb in these regions. The CLM involving the Triticeae consensus genetic map revealed that the above distribution of genes and recombination is the same in other Triticeae species. Because of a significant number of common markers, our CLM can be used for comparative mapping and to estimate physical distances among markers in many Poaceae species including rice and maize.

scholarly journals Construction of a High-Density Genetic Map for Pitaya Using the Whole Genome Resequencing Approach

Horticulturae ◽  
2021 ◽  
Vol 7 (12) ◽  
pp. 534
Author(s):  
Zhijiang Wu ◽  
Haiyan Deng ◽  
Guidong Liang ◽  
Xiaoying Ye ◽  
Yonghua Qin ◽  
...  
Keyword(s):  
Linkage Map ◽  
Genetic Map ◽  
Snp Markers ◽  
High Density ◽  
Genetic Maps ◽  
Fleshy Fruit ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Hylocereus Undatus ◽  
Whole Genome Resequencing

Pitaya (Hylocereus undatus) is one of the most economic fleshy fruit tree crops. This study aimed at producing a high-density linkage genetic map of pitaya based on the whole genome resequencing (WGrS) approach. For this purpose, a bi-parental F1 population of 198 individuals was generated and genotyped by WGrS. High-quality polymorphic 6434 single polymorphism nucleotide (SNP) markers were extracted and used to construct a high-density linkage map. A total of 11 linkage groups were resolved as expected in accordance with the chromosome number. The map length was 14,128.7 cM with an average SNP interval of 2.2 cM. Homology with the sequenced reference genome was described, and the physical and genetic maps were compared with collinearity analysis. This linkage map in addition to the available genomic resources will help for quantitative trait mapping, evolutionary studies and marker-assisted selection in the important Hylocereus species.

scholarly journals Construction of a High-Density Genetic Map and Mapping of Firmness in Grapes (Vitis vinifera L.) Based on Whole-Genome Resequencing

2020 ◽  
Vol 21 (3) ◽  
pp. 797 ◽  
Author(s):  
Jianfu Jiang ◽  
Xiucai Fan ◽  
Ying Zhang ◽  
Xiaoping Tang ◽  
Xiaomei Li ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Genetic Map ◽  
High Density ◽  
Pcr Analysis ◽  
Vitis Vinifera L ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Phenotypic Data ◽  
Table Grapes ◽  
Whole Genome Resequencing

Berry firmness is one of the most important quality traits in table grapes. The underlying molecular and genetic mechanisms for berry firmness remain unclear. We constructed a high-density genetic map based on whole-genome resequencing to identify loci associated with berry firmness. The genetic map had 19 linkage groups, including 1662 bin markers (26,039 SNPs), covering 1463.38 cM, and the average inter-marker distance was 0.88 cM. An analysis of berry firmness in the F1 population and both parents for three consecutive years revealed continuous variability in F1, with a distribution close to the normal distribution. Based on the genetic map and phenotypic data, three potentially significant quantitative trait loci (QTLs) related to berry firmness were identified by composite interval mapping. The contribution rate of each QTL ranged from 21.5% to 28.6%. We identified four candidate genes associated with grape firmness, which are related to endoglucanase, abscisic acid (ABA), and transcription factors. A qRT-PCR analysis revealed that the expression of abscisic-aldehyde oxidase-like gene (VIT_18s0041g02410) and endoglucanase 3 gene (VIT_18s0089g00210) in Muscat Hamburg was higher than in Crimson Seedless at the veraison stage, which was consistent with that of parent berry firmness. These results confirmed that VIT_18s0041g02410 and VIT_18s0089g00210 are candidate genes associated with berry firmness.

scholarly journals Construction of a high-density SNP-based genetic map and identification of fruit-related QTLs and candidate genes in peach [Prunus persica (L.) Batsch]

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Pei Shi ◽  
Ze Xu ◽  
Shaoyu Zhang ◽  
Xianju Wang ◽  
Xiaofei Ma ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Genetic Map ◽  
Fruit Quality ◽  
Prunus Persica ◽  
Expression Profiles ◽  
Genetic Research ◽  
High Density ◽  
Genetic Maps ◽  
Eating Quality ◽  
Soluble Solid Content

Abstract Background High-density genetic mapping is a valuable tool for mapping loci that control specific traits for perennial fruit trees. Peach is an economically important fruit tree and a model Rosaceae species for genomic and genetic research. In peach, even though many molecular markers, genetic maps and QTL mappings have been reported, further research on the improvement of marker numbers, map densities, QTL accuracy and candidate gene identification is still warranted. Results A high-density single nucleotide polymorphism (SNP)-based peach linkage map was constructed using specific locus amplified fragment sequencing (SLAF-seq). This genetic map consisted of 7998 SLAF markers, spanning 1098.79 cM with an average distance of 0.17 cM between adjacent markers. A total of 40 QTLs and 885 annotated candidate genes were detected for 10 fruit-related traits, including fruit weight (FW), fruit diameter (FD), percentage of red skin colour (PSC), eating quality (EQ), fruit flavour (FV), red in flesh (RF), red around pit (RP), adherence to pit (AP), fruit development period (FDP) and fruit fibre content (FFC). Eighteen QTLs for soluble solid content (SSC) were identified along LGs 1, 4, 5, and 6 in 2015 and 2016, and 540 genes were annotated in QTL intervals. Thirty-two QTLs for fruit acidity content (FA) were detected on LG1, and 2, 4, 5, 6, and 1232 candidate genes were identified. The expression profiles of 2 candidate genes for SSC and 4 for FA were analysed in parents and their offspring. Conclusions We constructed a high-density genetic map in peach based on SLAF-seq, which may contribute to the identification of important agronomic trait loci. Ninety QTLs for 12 fruit-related traits were identified, most of which overlapped with previous reports, and some new QTLs were obtained. A large number of candidate genes for fruit-related traits were screened and identified. These results may improve our understanding of the genetic control of fruit quality traits and provide useful information in marker-assisted selection for fruit quality in peach breeding programmes.

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