scholarly journals Identification of fruit size associated quantitative trait loci featuring SLAF based high-density linkage map of goji berry (Lycium spp.)

2020 ◽  
Author(s):  
Fazal Rehman ◽  
Haiguang Gong ◽  
Zhong Li ◽  
Shaohua Zeng ◽  
Tianshun Yang ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Linkage Map ◽  
Genetic Map ◽  
De Novo ◽  
Fruit Size ◽  
Leaf Size ◽  
High Density ◽  
Potential Candidate ◽  
Goji Berry ◽  
High Density Linkage Map

Abstract Background: Goji (Lycium spp., 2n = 24) is a perennial woody plant bearing functional properties. Fruit size associated attributes are important for evaluating small-fruited goji berry and plant architecture. The domestication traits are regulated quantitatively in crop plants but fewer studies have attempted on genomic regions corresponding to the fruit traits.Results: In this study, we established high-resolution map using SLAF-seq for de novo SNPs detection, based on 305 F1 offspring derived from L. chinense and L. barbarum. This genetic map contained 3,495 SNP markers on 12 LGs, spanning 1,649.03 cM with 0.47 cM average interval. Female and male parents had sequencing depth of 72.43-fold and 60.43-fold, respectively, while 15.23-fold detected for individuals. Phenotype data were obtained for 2 years and included 3rd year data as an average. QTL mapping analysis resulted in 117 QTLs corresponding to all traits, of which 23 QTLs in 2 years and 6 QTLs in 3rd years were detected. 6 promising QTLs, qFW10-3.1, qFL10-2.1, qLL10-2.1, qLD10-2.1, qLD12-4.1 and qLA10-2.1 were discovered influencing fruit weight, fruit length and leaf size related attributes covering an interval ranged 13.74-76.61 cM on LG10 with peak LOD up to 14.21 and PVE 19.3%. Additionally, 3 QTLs, qFS-1, qFS-2 and qFF-1, targeting fruit sweetness and fruit firmness were also identified in this study. Strikingly, among stable QTLs, qFL10-2.1, was co-localized to qLL10-2.1, qLD10-2.1, qLA10-2.1 and harbored significantly similar markers distribution, while qLL10-2.1 was the major and stable QTL with LOD ranged from 8.71-14.21 and PVE 12.3-19.3%. As LG10 harbored most of the fruit and leaf size related QTLs, we might speculate that it could be a hotspot region regulating fruit size and plant architectures.Conclusions: This report highlighted that the high-density linkage map construction using SLAF-seq is an important means for profound QTL mapping approach. Substantially, we utilized highly saturated genetic map to find out genetic locus targeting fruit and leaf size related attributes under QTL mapping. Our results will shed light on domestication traits and further strengthen molecular and genetic underpinnings of goji berry. Moreover, these findings would facilitate to assemble reference genome, determining potential candidate genes and marker-assisted breeding.

scholarly journals Identification of fruit size associated quantitative trait loci featuring SLAF based high-density linkage map of goji berry (Lycium spp.)

2020 ◽  
Author(s):  
Fazal Rehman ◽  
Haiguang Gong ◽  
Zhong Li ◽  
Shaohua Zeng ◽  
Tianshun Yang ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Linkage Map ◽  
Quantitative Trait ◽  
De Novo ◽  
Fruit Size ◽  
Fruit Weight ◽  
Potential Candidate ◽  
Multiple Traits ◽  
Goji Berry ◽  
Trait Loci

Abstract Background: Goji (Lycium spp., 2n = 24) is a fruit bearing woody plant popular as a superfood for extensive medicinal and nutritional advantages. Fruit size associated attributes are important for evaluating small-fruited goji berry and plant architecture. The domestication traits are regulated quantitatively in crop plants but few studies have attempted on genomic regions corresponding to fruit traits. Results: In this study, we established high-resolution map using specific locus amplified fragment (SLAF) sequencing for de novo SNPs detection based on 305 F1 individuals derived from L. chinense and L. barbarum and performed quantitative trait loci (QTL) analysis of fruit size related traits in goji berry. The genetic map contained 3,495 SLAF markers on 12 LGs, spanning 1,649.03 cM with 0.47 cM average interval. Female and male parents and F1 individuals` sequencing depth was 111.85-fold and 168.72-fold and 35.80-fold, respectively. The phenotype data were collected for 2 successive years (2018-2019); however, two-year mean data were combined in an extra year (1819). Total 117 QTLs were detected corresponding to multiple traits, of which 78 QTLs in 2 individual years and 36 QTLs in extra year. 6 Promising QTLs (qFW10-6.1, qFL10-2.1, qLL10-2.1, qLD10-2.1, qLD12-4.1, qLA10-2.1) were discovered influencing fruit weight, fruit length and leaf related attributes covering an interval ranged from 27.32-71.59 cM on LG10 with peak LOD of 10.48 and 14.6% PVE. Three QTLs targeting fruit sweetness (qFS3-1, qFS5-2) and fruit firmness (qFF10-1) were also identified. Strikingly, various traits QTLs were overlapped on LG10, in particular, qFL10-2.1 was co-located with qLL10-2.1, qLD10-2.1 and qLA10-2.1 among stable QTLs, harbored tightly linked markers, while qLL10-1 was one major QTL with 14.21 highest LOD and 19.3% variance. As LG10 harbored important traits QTLs, we might speculate that it could be hotspot region regulating fruit size and plant architectures. Conclusions: This report highlighted the extremely saturated linkage map using SLAF-seq and novel loci contributing fruit size-related attributes in goji berry. Our results will shed light on domestication traits and further strengthen molecular and genetic underpinnings of goji berry; moreover, these findings would better facilitate to assemble the reference genome, determining potential candidate genes and marker-assisted breeding.

scholarly journals Identification of fruit size associated quantitative trait loci featuring SLAF based high-density linkage map of goji berry (Lycium spp.)

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Fazal Rehman ◽  
Haiguang Gong ◽  
Zhong Li ◽  
Shaohua Zeng ◽  
Tianshun Yang ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Linkage Map ◽  
Quantitative Trait ◽  
De Novo ◽  
Fruit Size ◽  
Fruit Weight ◽  
Potential Candidate ◽  
Multiple Traits ◽  
Goji Berry ◽  
Trait Loci

Abstract Background Goji (Lycium spp., 2n = 24) is a fruit bearing woody plant popular as a superfood for extensive medicinal and nutritional advantages. Fruit size associated attributes are important for evaluating small-fruited goji berry and plant architecture. The domestication traits are regulated quantitatively in crop plants but few studies have attempted on genomic regions corresponding to fruit traits. Results In this study, we established high-resolution map using specific locus amplified fragment (SLAF) sequencing for de novo SNPs detection based on 305 F1 individuals derived from L. chinense and L. barbarum and performed quantitative trait loci (QTL) analysis of fruit size related traits in goji berry. The genetic map contained 3495 SLAF markers on 12 LGs, spanning 1649.03 cM with 0.47 cM average interval. Female and male parents and F1 individuals` sequencing depth was 111.85-fold and 168.72-fold and 35.80-fold, respectively. The phenotype data were collected for 2 successive years (2018–2019); however, two-year mean data were combined in an extra year (1819). Total 117 QTLs were detected corresponding to multiple traits, of which 78 QTLs in 2 individual years and 36 QTLs in extra year. Six Promising QTLs (qFW10–6.1, qFL10–2.1, qLL10–2.1, qLD10–2.1, qLD12–4.1, qLA10–2.1) were discovered influencing fruit weight, fruit length and leaf related attributes covering an interval ranged from 27.32–71.59 cM on LG10 with peak LOD of 10.48 and 14.6% PVE. Three QTLs targeting fruit sweetness (qFS3–1, qFS5–2) and fruit firmness (qFF10–1) were also identified. Strikingly, various traits QTLs were overlapped on LG10, in particular, qFL10–2.1 was co-located with qLL10–2.1, qLD10–2.1 and qLA10–2.1 among stable QTLs, harbored tightly linked markers, while qLL10–1 was one major QTL with 14.21 highest LOD and 19.3% variance. As LG10 harbored important traits QTLs, we might speculate that it could be hotspot region regulating fruit size and plant architectures. Conclusions This report highlights the extremely saturated linkage map using SLAF-seq and novel loci contributing fruit size-related attributes in goji berry. Our results will shed light on domestication traits and further strengthen molecular and genetic underpinnings of goji berry; moreover, these findings would better facilitate to assemble the reference genome, determining potential candidate genes and marker-assisted breeding.

scholarly journals Identification of fruit size associated quantitative trait loci featuring SLAF based high-density linkage map of goji berry (Lycium spp.)

2020 ◽  
Author(s):  
Fazal Rehman ◽  
Haiguang Gong ◽  
Zhong Li ◽  
Shaohua Zeng ◽  
Tianshun Yang ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Linkage Map ◽  
Quantitative Trait ◽  
De Novo ◽  
Fruit Size ◽  
Fruit Weight ◽  
Potential Candidate ◽  
Multiple Traits ◽  
Goji Berry ◽  
Trait Loci

Abstract Background: Goji (Lycium spp., 2n = 24) is a fruit bearing woody plant popular as a superfood for extensive medicinal and nutritional advantages. Fruit size associated attributes are important for evaluating small-fruited goji berry and plant architecture. The domestication traits are regulated quantitatively in crop plants but few studies have attempted on genomic regions corresponding to fruit traits.Results: In this study, we established high-resolution map using specific locus amplified fragment (SLAF) sequencing for de novo SNPs detection based on 305 F1 individuals derived from L. chinense and L. barbarum and performed quantitative trait loci (QTL) analysis of fruit size related traits in goji berry. The genetic map contained 3,495 SLAF markers on 12 LGs, spanning 1,649.03 cM with 0.47 cM average interval. Female and male parents and F1 individuals` sequencing depth was 111.85-fold and 168.72-fold and 35.80-fold, respectively. The phenotype data were collected for 2 successive years (2018-2019); however, two-year mean data were combined in an extra year (1819). Total 117 QTLs were detected corresponding to multiple traits, of which 78 QTLs in 2 individual years and 36 QTLs in extra year. 6 Promising QTLs (qFW10-6.1, qFL10-2.1, qLL10-2.1, qLD10-2.1, qLD12-4.1, qLA10-2.1) were discovered influencing fruit weight, fruit length and leaf related attributes covering an interval ranged from 27.32-71.59 cM on LG10 with peak LOD of 10.48 and 14.6% PVE. Three QTLs targeting fruit sweetness (qFS3-1, qFS5-2) and fruit firmness (qFF10-1) were also identified. Strikingly, various traits QTLs were overlapped on LG10, in particular, qFL10-2.1 was co-located with qLL10-2.1, qLD10-2.1 and qLA10-2.1 among stable QTLs, harbored tightly linked markers, while qLL10-1 was one major QTL with 14.21 highest LOD and 19.3% variance. As LG10 harbored important traits QTLs, we might speculate that it could be hotspot region regulating fruit size and plant architectures.Conclusions: This report highlights the extremely saturated linkage map using SLAF-seq and novel loci contributing fruit size-related attributes in goji berry. Our results will shed light on domestication traits and further strengthen molecular and genetic underpinnings of goji berry; moreover, these findings would better facilitate to assemble the reference genome, determining potential candidate genes and marker-assisted breeding.

scholarly journals High-Density Genetic Map Construction and Identification of QTLs Controlling Leaf Abscission Trait in Poncirus trifoliata

2021 ◽  
Vol 22 (11) ◽  
pp. 5723
Author(s):  
Yuan-Yuan Xu ◽  
Sheng-Rui Liu ◽  
Zhi-Meng Gan ◽  
Ren-Fang Zeng ◽  
Jin-Zhi Zhang ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Linkage Map ◽  
Genetic Map ◽  
Expression Patterns ◽  
High Density ◽  
Poncirus Trifoliata ◽  
Leaf Abscission ◽  
Comparative Genomic ◽  
Map Comparison ◽  
Genomic Studies

A high-density genetic linkage map is essential for genetic and genomic studies including QTL mapping, genome assembly, and comparative genomic analysis. Here, we constructed a citrus high-density linkage map using SSR and SNP markers, which are evenly distributed across the citrus genome. The integrated linkage map contains 4163 markers with an average distance of 1.12 cM. The female and male linkage maps contain 1478 and 2976 markers with genetic lengths of 1093.90 cM and 1227.03 cM, respectively. Meanwhile, a genetic map comparison demonstrates that the linear order of common markers is highly conserved between the clementine mandarin and Poncirus trifoliata. Based on this high-density integrated citrus genetic map and two years of deciduous phenotypic data, two loci conferring leaf abscission phenotypic variation were detected on scaffold 1 (including 36 genes) and scaffold 8 (including 107 genes) using association analysis. Moreover, the expression patterns of 30 candidate genes were investigated under cold stress conditions because cold temperature is closely linked with the deciduous trait. The developed high-density genetic map will facilitate QTL mapping and genomic studies, and the localization of the leaf abscission deciduous trait will be valuable for understanding the mechanism of this deciduous trait and citrus breeding.

scholarly journals Effect of marker segregation distortion on high density linkage map construction and QTL mapping in Soybean (Glycine max L.)

Heredity ◽  
2019 ◽  
Vol 123 (5) ◽  
pp. 579-592 ◽  
Author(s):  
Jian-Fang Zuo ◽  
Yuan Niu ◽  
Peng Cheng ◽  
Jian-Ying Feng ◽  
Shi-Feng Han ◽  
...  
Keyword(s):  
Glycine Max ◽  
Qtl Mapping ◽  
Linkage Map ◽  
Segregation Distortion ◽  
High Density ◽  
Map Construction ◽  
Glycine Max L ◽  
Marker Segregation Distortion ◽  
High Density Linkage Map

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 A high-density linkage map and QTL mapping of fruit-related traits in pumpkin (Cucurbita moschata Duch.)

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Yu-Juan Zhong ◽  
Yang-Yang Zhou ◽  
Jun-Xing Li ◽  
Ting Yu ◽  
Ting-Quan Wu ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Linkage Map ◽  
High Density ◽  
Cucurbita Moschata ◽  
High Density Linkage Map

scholarly journals A High Density Linkage Map Facilitates QTL Mapping of Flowering Time in Brassica rapa

2016 ◽  
Vol 2 (4) ◽  
pp. 217-223 ◽  
Author(s):  
Jing Liu ◽  
Bo Liu ◽  
Feng Cheng ◽  
Jianli Liang ◽  
Xiaowu Wang ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Linkage Map ◽  
Flowering Time ◽  
Brassica Rapa ◽  
High Density ◽  
High Density Linkage Map

scholarly journals Detection of QTLs for panicle-related traits using an indica × japonica recombinant inbred line population in rice

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12504
Author(s):  
Guan Li ◽  
Yichen Cheng ◽  
Man Yin ◽  
Jinyu Yang ◽  
Jiezheng Ying ◽  
...  
Keyword(s):  
Grain Yield ◽  
Linkage Map ◽  
Genetic Map ◽  
Inbred Line ◽  
Recombinant Inbred Line ◽  
Recombinant Inbred Line Population ◽  
Recombinant Inbred ◽  
High Density ◽  
Rice Grain ◽  
High Density Linkage Map

Background The panicle is the most important organ in rice, and all the panicle-related traits are correlated with rice grain yield. Understanding the underlying genetic mechanisms controlling panicle development is very important for improving rice production. Methods Nine panicle-related traits including heading date, panicle length, number of primary branches, number of secondary branches, number of grains per panicle, number of panicles per plant, number of filled grains per plant, seed-setting rate, and grain yield per plant were investigated. To map the quantitative trait loci (QTLs) for the nine panicle-related traits, a PCR-based genetic map with 208 markers (including 121 simple sequence repeats and 87 InDels) and a high-density linkage map with 18,194 single nucleotide polymorphism (SNP) markers were both used. Results Using a recombinant inbred line population derived from an indica variety Huanghuazhan and a japonica line Jizi 1560, a total of 110 and 112 QTLs were detected for panicle-related traits by PCR-based genetic map and by high-density linkage map, respectively. Most of the QTLs were clustered on chromosomes 1, 2, 3, 6, and 7 while no QTLs were detected on chromosome 10. Almost all the QTLs with LOD values of more than 5.0 were repeatedly detected, indicating the accuracy of the two methods and the stability of the QTL effects. No genes for panicle-related traits have been previously reported in most of these regions. QTLs found in JD1006–JD1007 and RM1148–RM5556 with high LOD and additive values deserved further research. The results of this study are beneficial for marker-assisted breeding and provide research foundation for further fine-mapping and cloning of these QTLs for panicle-related traits.

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