scholarly journals QTL mapping for growth-related traits by constructing the first genetic linkage map in Simao pine

2020 ◽  
Author(s):  
dawei Wang ◽  
chen Shi ◽  
Siguang Li ◽  
Hongyan Tang ◽  
Chenzhong He ◽  
...  
Keyword(s):  
Linkage Map ◽  
Genetic Map ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Phenotypic Variance ◽  
Basal Diameter ◽  
Exploitation And Utilization ◽  
Information Construction ◽  
Genomic Studies ◽  
Needle Diameter

Abstract Background: Simao pine is one of the primary economic tree species for resin and timber production in southwest China. The exploitation and utilization of Simao pine are constrained by the relatively lacking of genetic information. Construction a fine genetic linkage map and detecting quantitative trait locis (QTLs) for growth-related traits is a prerequisite section of Simao Pine's molecular breeding program. Results: In our study, a high-resolution Simao pine genetic map employed specific locus amplified fragment sequencing (SLAF-seq) technology and based on an F1 pseudo-testcross population has been constructed. There were 11,544 SNPs assigned to 12 linkage groups (LGs), and the total length of the map was 2,062.85 cM with a mean distance of 0.37 cM between markers. According to the phenotypic variation analysis for three consecutive years, a total of seventeen QTLs for four traits were detected. Among 17 QTLs, there were six for plant height (Dh.16.1, Dh16.2, Dh17.1, Dh18.1-3), five for basal diameter (Dbd.17.1-5), four for needle length (Dnl17.1-3, Dnl18.1) and two for needle diameter (Dnd17.1 and Dnd18.1) respectively. These QTLs individually explained phenotypic variance from 11.0-16.3 %, and the logarithm of odds (LOD) value ranged from 2.52 to 3.87. Conclusions: In our study, a fine genetic map of Simao pine applied the technology of SLAF-seq has been constructed for the first time. Based on the map, a total of 17 QTLs for four growth-related traits were identified. It provides helpful information for genomic studies and marker-assisted selection (MAS) in Simao pine.

scholarly journals QTL Mapping for Growth-Related Traits by Constructing the First Genetic Linkage Map in Simao pine

2020 ◽  
Author(s):  
dawei Wang ◽  
chen Shi ◽  
Siguang Li ◽  
Hongyan Tang ◽  
Chenzhong He ◽  
...  
Keyword(s):  
Linkage Map ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Phenotypic Variance ◽  
Basal Diameter ◽  
Exploitation And Utilization ◽  
Information Construction ◽  
Genomic Studies ◽  
Specific Locus ◽  
Needle Diameter

Abstract Simao pine is one of primary economic tree species for resin and timber production in southwest China, the exploitation and utilization are constrained by relatively lacking the genetic information. Construction a fine genetic linkage map and detecting QTLs for growth-related traits is an important section in molecular breeding program for Simao Pine. In our study, a high-resolution Simao pine genetic map employing specific locus amplified fragment sequencing (SLAF-seq) with an F1 population has been constructed. There were 11,544 SNPs assigned to 12 linkage groups in the map, and the total length of the map was 2,062.85 cM with a mean distance of 0.37 cM between markers. According to the phenotypic variation analysis during three consecutive years, seventeen QTLs for four traits which including six for plant height (Dh.16.1, Dh16.2, Dh17.1, Dh18.1-3), five for basal diameter (Dbd.17.1-5), four for needle length (Dnl17.1-3, Dnl18.1) and two for needle diameter (Dnd17.1 and Dnd18.1) were identified. These QTLs individually explained phenotypic variance from 11.0-16.3 %, and the LOD value ranged from 2.52 to 3.87. The result in this study provide helpful information for genomic studies and marker-assisted selection (MAS) in Simao pine.

scholarly journals A high-density genetic map construction and sex-related loci identification in Chinese Giant salamander

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Qiaomu Hu ◽  
Yang Liu ◽  
Xiaolin Liao ◽  
Haifeng Tian ◽  
Xiangshan Ji ◽  
...  
Keyword(s):  
Linkage Map ◽  
Genetic Map ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Economic Value ◽  
Genetic Research ◽  
High Density ◽  
Amphibian Species ◽  
Genomic Studies ◽  
Chinese Giant Salamander

Abstract Background The Chinese giant salamander Andrias davidianus is an important amphibian species in China because of its increasing economic value, protection status and special evolutionary position from aquatic to terrestrial animal. Its large genome presents challenges to genetic research. Genetic linkage mapping is an important tool for genome assembly and determination of phenotype-related loci. Results In this study, we constructed a high-density genetic linkage map using ddRAD sequencing technology to obtain SNP genotyping data of members from an full-sib family which sex had been determined. A total of 10,896 markers were grouped and oriented into 30 linkage groups, representing 30 chromosomes of A. davidianus. The genetic length of LGs ranged from 17.61 cM (LG30) to 280.81 cM (LG1), with a mean inter-locus distance ranging from 0.11(LG3) to 0.48 cM (LG26). The total genetic map length was 2643.10 cM with an average inter-locus distance of 0.24 cM. Three sex-related loci and four sex-related markers were found on LG6 and LG23, respectively. Conclusion We constructed the first High-density genetic linkage map and identified three sex-related loci in the Chinese giant salamander. Current results are expected to be a useful tool for future genomic studies aiming at the marker-assisted breeding of the species.

scholarly journals A high-density SNP-based genetic map and several economic traits-related loci in Pelteobagrus vachelli

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Guosong Zhang ◽  
Jie Li ◽  
Jiajia Zhang ◽  
Xia Liang ◽  
Tao Wang ◽  
...  
Keyword(s):  
Sex Determination ◽  
Linkage Map ◽  
Candidate Genes ◽  
Genetic Map ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
High Density ◽  
Hypoxia Tolerance ◽  
Genome Wide ◽  
Pelteobagrus Vachelli

Abstract Background A high-density genetic linkage map is essential for QTL fine mapping, comparative genome analysis, identification of candidate genes and marker-assisted selection in aquaculture species. Pelteobagrus vachelli is a very popular commercial species in Asia. However, some specific characters hindered achievement of the traditional selective breeding based on phenotypes, such as lack of large-scale genomic resource and short of markers tightly associated with growth, sex determination and hypoxia tolerance related traits. Results By making use of 5059 ddRAD markers in P. vachelli, a high-resolution genetic linkage map was successfully constructed. The map’ length was 4047.01 cM by using an interval of 0.11 cm, which is an average marker standard. Comparative genome mapping revealed that a high proportion (83.2%) of markers with a one-to-one correspondence were observed between P. vachelli and P. fulvidraco. Based on the genetic map, 8 significant genome-wide QTLs for 4 weight, 1 body proportion, 2 sex determination, and 1 hypoxia tolerance related traits were detected on 4 LGs. Some SNPs from these significant genome-wide QTLs were observably associated with these phenotypic traits in other individuals by Kompetitive Allele Specific PCR. In addition, two candidate genes for weight, Sipa1 and HSD11B2, were differentially expressed between fast-, medium- and slow-growing P. vachelli. Sema7a, associated with hypoxia tolerance, was induced after hypoxia exposure and reoxygenation. Conclusions We mapped a set of suggestive and significant QTLs as well as candidate genes for 12 growth, 1 sex determination and 1 hypoxia tolerance related traits based on a high-density genetic linkage map by making use of SNP markers for P. fulvidraco. Our results have offered a valuable method about the much more efficient production of all-male, fast growth and hypoxia tolerance P. vachelli for the aquaculture industry.

Construction of a high-density linkage map and QTL analysis for pistil abortion in apricot (Prunus armeniaca L.)

2019 ◽  
Vol 99 (5) ◽  
pp. 599-610
Author(s):  
Junhuan Zhang ◽  
Haoyuan Sun ◽  
Li Yang ◽  
Fengchao Jiang ◽  
Meiling Zhang ◽  
...  
Keyword(s):  
Linkage Map ◽  
Genetic Map ◽  
Qtl Analysis ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Prunus Armeniaca ◽  
High Density ◽  
Pistil Abortion ◽  
Genomic Study ◽  
Prunus Armeniaca L

A high-density genetic map of apricot (Prunus armeniaca L.) was constructed using an F1 population constructed by crossing two main Chinese cultivars ‘Chuanzhihong’ and ‘Luotuohuang’, coupled with a recently developed reduced representation library (RRL) sequencing. The average sequencing depth was 38.97 in ‘Chuanzhihong’ (female parent), 33.05 in ‘Luotuohuang’ (male parent), and 8.91 in each progeny. Based on the sequencing data, 12 451 polymorphic markers were developed and used in the construction of the genetic linkage map. The final map of apricot comprised eight linkage groups, including 1991 markers, and covered 886.25 cM of the total map length. The average distance between adjacent markers was narrowed to 0.46 cM. Gaps larger than 5 cM only accounted for <0.33%. To our knowledge, this map is the densest genetic linkage map that is currently available for apricot research. It is a valuable linkage map for quantitative trait loci (QTLs) identification of important agronomic traits. Moreover, the high marker density and well-ordered markers that this linkage map provides will be useful for molecular breeding of apricot as well. In this study, we applied this map in the QTL analysis of an important agronomic trait, pistil abortion. Several QTLs were detected and mapped respectively to the middle regions of LG5 (51.005∼59.4 cM) and LG6 (72.884∼76.562 cM), with nine SLAF markers closely linked to pistil abortion. The high-density genetic map and QTLs detected in this study will facilitate marker-assisted breeding and apricot genomic study.

scholarly journals High-Density GBS-Based Genetic Linkage Map Construction and QTL Identification Associated With Yellow Mosaic Disease Resistance in Bitter Gourd (Momordica charantia L.)

2021 ◽  
Vol 12 ◽  
Author(s):  
Gurpreet Kaur ◽  
Mamta Pathak ◽  
Deepak Singla ◽  
Abhishek Sharma ◽  
Parveen Chhuneja ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Linkage Map ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Snp Markers ◽  
Mosaic Disease ◽  
Bitter Gourd ◽  
Phenotypic Variance ◽  
Spring Season ◽  
Yellow Mosaic Disease

Yellow mosaic disease (YMD) in bitter gourd (Momordica charantia) is a devastating disease that seriously affects its yield. Although there is currently no effective method to control the disease, breeding of resistant varieties is the most effective and economic option. Moreover, quantitative trait locus (QTL) associated with resistance to YMD has not yet been reported. With the objective of mapping YMD resistance in bitter gourd, the susceptible parent “Punjab-14” and the resistant parent “PAUBG-6” were crossed to obtain F4 mapping population comprising 101 individuals. In the present study, the genotyping by sequencing (GBS) approach was used to develop the genetic linkage map. The map contained 3,144 single nucleotide polymorphism (SNP) markers, consisted of 15 linkage groups, and it spanned 2415.2 cM with an average marker distance of 0.7 cM. By adopting the artificial and field inoculation techniques, F4:5 individuals were phenotyped for disease resistance in Nethouse (2019), Rainy (2019), and Spring season (2020). The QTL analysis using the genetic map and phenotyping data identified three QTLs qYMD.pau_3.1, qYMD.pau_4.1, and qYMD.pau_5.1 on chromosome 3, 4, and 5 respectively. Among these, qYMD.pau_3.1, qYMD.pau_4.1 QTLs were identified during the rainy season, explaining the 13.5 and 21.6% phenotypic variance respectively, whereas, during the spring season, qYMD.pau_4.1 and qYMD.pau_5.1 QTLs were observed with 17.5 and 22.1% phenotypic variance respectively. Only one QTL qYMD.pau_5.1 was identified for disease resistance under nethouse conditions with 15.6% phenotypic variance. To our knowledge, this is the first report on the identification of QTLs associated with YMD resistance in bitter gourd using SNP markers. The information generated in this study is very useful in the future for fine-mapping and marker-assisted selection for disease resistance.

scholarly journals 1. A genetic linkage map of Pinus massoniana based on SRAP, SSR and ESTP markers

2014 ◽  
Vol 63 (1-6) ◽  
pp. 1-8 ◽  
Author(s):  
Wenxia Chen ◽  
Mu Cao ◽  
Yuanxiu Wang ◽  
Zhichun Zhou ◽  
Li-An Xu
Keyword(s):  
Linkage Map ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Mapping Population ◽  
Southern China ◽  
Pinus Massoniana ◽  
Genetic Maps ◽  
Masson Pine ◽  
F1 Progeny ◽  
Genomic Studies

Abstract Pinus massoniana (masson pine) is the most important native pine in southern China. High-density genetic maps have not been constructed for the species. In this study, a genetic linkage map with 251 markers (47 SSRs, 23 ESTPs and 181 SRAPs) was constructed using a F1 progeny mapping population derived from controlled pollination of two parents of different provenances. At LOD 7.0, a total of 17 linkage groups were constructed with twelve groups having nine or more markers and five other groups of two to four markers each. The total map length was 1,956 cM with an average of 8.4 cM among individual loci. The current linkage map represented 93% of the estimated genome length of 2,114 cM for masson pine. Such linkage map are useful for future genomic studies of masson pine including comparative mapping in Pinaceae and quantitative trait loci (QTL) mapping for economically important traits.

High-density Genetic Linkage Map Construction in Sunflower (Helianthus annuus L.) Using SNP and SSR Markers

2021 ◽  
Vol 15 (8) ◽  
pp. 889-897
Author(s):  
Pin Lyu ◽  
Jianhua Hou ◽  
Haifeng Yu ◽  
Huimin Shi
Keyword(s):  
Linkage Map ◽  
Helianthus Annuus ◽  
Ssr Markers ◽  
Genetic Map ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Snp Markers ◽  
High Density ◽  
Helianthus Annuus L ◽  
Density Maps

Background: Sunflower (Helianthus annuus L.) is an important oil crop only after soybean, canola and peanuts. A high-quality genetic map is the foundation of marker-assisted selection (MAS). However, for this species, the high-density maps have been reported limitedly. Objective: In this study, we proposed the construction of a high-density genetic linkage map by the F7 population of sunflowers using SNP and SSR Markers. Methods: The SLAF-seq strategy was employed to further develop SNP markers with SSR markers to construct the high-density genetic map by the HighMap software. Results: A total of 1,138 million paired-end reads (226Gb) were obtained and 518,900 SLAFs were detected. Of the polymorphic SLAFs, 2,472,245 SNPs were developed and finally, 5,700 SNPs were found to be ideal to construct a genetic map after filtering. The final high-density genetic map included 4,912 SNP and 93 SSR markers distributed in 17 linkage groups (LGs) and covered 2,425.05 cM with an average marker interval of 0.49 cM. Conclusion: The final result demonstrated that the SLAF-seq strategy is suitable for SNP markers detection. The genetic map reported in this study can be considered as one of the most highdensity genetic linkage maps of sunflower and could lay a foundation for quantitative trait loci (QTLs) fine mapping or map-based gene cloning.

Construction of genetic linkage map and mapping of QTL for seed color in Brassica rapa

Genome ◽  
2012 ◽  
Vol 55 (12) ◽  
pp. 813-823 ◽  
Author(s):  
Berisso Kebede ◽  
Kuljit Cheema ◽  
David L. Greenshields ◽  
Changxi Li ◽  
Gopalan Selvaraj ◽  
...  
Keyword(s):  
Linkage Map ◽  
Ssr Markers ◽  
Brassica Rapa ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Recombinant Inbred Lines ◽  
Phenotypic Variance ◽  
Environment Interaction ◽  
Seed Color ◽  
A Genome

A genetic linkage map of Brassica rapa L. was constructed using recombinant inbred lines (RILs) derived from a cross between yellow-seeded cultivar Sampad and a yellowish brown seeded inbred line 3-0026.027. The RILs were evaluated for seed color under three conditions: field plot, greenhouse, and controlled growth chambers. Variation for seed color in the RILs ranged from yellow, like yellow sarson, to dark brown/black even though neither parent had shown brown/black colored seeds. One major QTL (SCA9-2) and one minor QTL (SCA9-1) on linkage group (LG) A9 and two minor QTL (SCA3-1, SCA5-1) on LG A3 and LG A5, respectively, were detected. These collectively explained about 67% of the total phenotypic variance. SCA9-2 mapped in the middle of LG A9, explained about 55% phenotypic variance, and consistently expressed in all environments. The second QTL on LG A9 was ∼70 cM away from SCA9-2, suggesting that independent assortment of these QTLs is possible. A digenic epistatic interaction was found between the two main effect QTL on LG A9; and the epistasis × environment interaction was nonsignificant, suggesting stability of the interaction across the environments. The QTL effect on LG A9 was validated using simple sequence repeat (SSR) markers from the two QTL regions of this LG on a B1S1 population (F1 backcrossed to Sampad followed by self-pollination) segregating for brown and yellow seed color, and on their self-pollinated progenies (B1S2). The SSR markers from the QTL region SCA9-2 showed a stronger linkage association with seed color as compared with the marker from SCA9-1. This suggests that the QTL SCA9-2 is the major determinant of seed color in the A genome of B. rapa.

scholarly journals A high-density SNP-based genetic map in Pelteobagrus vachelli and mapping of growth, sex determination and hypoxia tolerance related loci

2019 ◽  
Author(s):  
Guosong Zhang ◽  
Jie Li ◽  
Jiajia Zhang ◽  
Xia Liang ◽  
Tao Wang ◽  
...  
Keyword(s):  
Sex Determination ◽  
Linkage Map ◽  
Candidate Genes ◽  
Genetic Map ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
High Density ◽  
Hypoxia Tolerance ◽  
Genome Wide ◽  
Pelteobagrus Vachelli

Abstract Background: As is known to all, when we are doing QTL fine mapping, analyzing comparative genome, identifying candidate genes, making marker-assisted selection in aquaculture species, the high-density genetic linkage map is of great significance. Pelteobagrus vachelli is a very popular commercial species in Asia. However, some specific characters made it difficult to do traditional selective breeding based on phenotypes. For instance, potential problems include lacking in genomic resource which is in large scale and short of markers that is related tightly to growth, sex determination and hypoxia tolerance related traits. Results: By making use of 5059 ddRAD markers in P. vachelli，a high-resolution genetic linkage map was successfully constructed. The map’ length was 4047.01 cM by using an interval of 0.11 cm, which is an average marker standard. It is reflected that bu using comparative genome mapping, a large majority (83.2%) of markers with a one-to-one correspondence were observed between P. vachelli and P. fulvidraco. Based on the genetic map, 8 significant genome-wide QTLs for 4 weight, 1 body proportion, 2 sex determination, and 1 hypoxia tolerance related traits were detected on 4 LGs. Some SNPs from these significant genome-wide QTLs were observably associated with these phenotypic traits in other individuals by Kompetitive Allele Specific PCR. In addition, two candidate gene for weight, Sipa1 and HSD11B2, were differentially expressed between fast-, medium- and slow-growing P. vachelli. Sema7a, associated with hypoxia tolerance, was induced after hypoxia exposure and reoxygenation. Conclusions: We mapped a set of suggestive and significant QTLs as well as candidate genes for 12 growth, 1 sex determination and 1 hypoxia tolerance related traits based on a high-density genetic linkage map by making use of SNP markers for P. fulvidraco. Our results have offered a valuable method about the much more efficient production of all-male, fast growth and hypoxia tolerance P. vachelli for the aquaculture industry.

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