scholarly journals Construction of SSR linkage maps and identification of QTL for resistance to root rot in sweetpotato (Ipomoea batatas (L.) Lam.)

2020 ◽  
Author(s):  
Zhimin Ma ◽  
Wenchuan Gao ◽  
Lanfu Liu ◽  
Minghui Liu ◽  
Ning Zhao ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Root Rot ◽  
Genetic Linkage ◽  
Practical Significance ◽  
Linkage Maps ◽  
Linkage Groups ◽  
Resistant Varieties ◽  
Marker Distance ◽  
Average Marker Distance ◽  
Map Distance

Abstract Background: Sweetpotato root rot is a devastating disease caused by Fusarium solani that causes significant yield losses of sweetpotato in China. There is currently no effective method to control the disease. The breeding of resistant varieties is the most effective and economic way to control the disease. To date, quantitative trait locus (QTL) for resistance to root rot have not been reported and the biological mechanisms of resistance remain unclear in sweetpotato. Thus, it is necessary and worthwhile to identify resistance loci to help develop disease-resistant varieties. Results: In this study, we constructed genetic linkage maps of sweetpotato using a mapping population consisting of 300 individuals derived from a cross between Jizishu 1 and Longshu 9 by simple sequence repeat (SSR) markers, and mapped seven QTLs for resistance to root rot. In total, 484 and 573 polymorphic SSR markers were grouped into 90 linkage groups for Jizishu 1 and Longshu 9, respectively. The total map distance for Jizishu 1 was 3,974.24 cM, with an average marker distance of 8.23 cM. The total map distance for Longshu 9 was 5,163.35 cM, with an average marker distance of 9.01 cM. Five QTLs ( qRRM_1 , qRRM_2 , qRRM_3, qRRM_4 , and qRRM_5 ) were located in five linkage groups of Jizishu 1 map explaining 52.6-57.0% of the variation. Two QTLs ( qRRF_1 and qRRF_2 ) were mapped on two linkage groups of Longshu 9 explaining 57.6% and 53.6% of the variation. 71.4 % of the QTLs had a positive effect on the variation. Three of the seven QTLs, qRRM_3 , qRRF_1 , and qRRF_2 , were colocalized with markers IES43-5mt, IES68-6fs**, and IES108-1fs, respectively. Conclusions: To our knowledge, this is the first report on the construction of a genetic linkage map for purple sweetpotato (Jizishu 1) and the identification of QTLs associated with resistance to root rot in sweetpotato using SSR markers. These QTLs will have practical significance for the fine mapping of root rot resistance genes and play an important role in sweetpotato marker-assisted breeding.

scholarly journals Construction of SSR linkage maps and identification of QTL for resistance to root rot in sweetpotato (Ipomoea batatas (L.) Lam.)

2020 ◽  
Author(s):  
Zhimin Ma ◽  
Wenchuan Gao ◽  
Lanfu Liu ◽  
Minghui Liu ◽  
Ning Zhao ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Root Rot ◽  
Genetic Linkage ◽  
Practical Significance ◽  
Linkage Maps ◽  
Linkage Groups ◽  
Resistant Varieties ◽  
Marker Distance ◽  
Average Marker Distance ◽  
Map Distance

Abstract Background: Sweetpotato root rot is a devastating disease caused by Fusarium solani that causes significant yield losses of sweetpotato in China. There is currently no effective method to control the disease. The breeding of resistant varieties is the most effective and economic way to control the disease. To date, quantitative trait locus (QTL) for resistance to root rot have not been reported and the biological mechanisms of resistance remain unclear in sweetpotato. Thus, it is necessary and worthwhile to identify resistance loci to help develop disease-resistant varieties. Results: In this study, we constructed genetic linkage maps of sweetpotato using a mapping population consisting of 300 individuals derived from a cross between Jizishu 1 and Longshu 9 by simple sequence repeat (SSR) markers, and mapped seven QTLs for resistance to root rot. In total, 484 and 573 polymorphic SSR markers were grouped into 90 linkage groups for Jizishu 1 and Longshu 9, respectively. The total map distance for Jizishu 1 was 3,974.24 cM, with an average marker distance of 8.23 cM. The total map distance for Longshu 9 was 5,163.35 cM, with an average marker distance of 9.01 cM. Five QTLs ( qRRM_1 , qRRM_2 , qRRM_3, qRRM_4 , and qRRM_5 ) were located in five linkage groups of Jizishu 1 map explaining 52.6-57.0% of the variation. Two QTLs ( qRRF_1 and qRRF_2 ) were mapped on two linkage groups of Longshu 9 explaining 57.6% and 53.6% of the variation. 71.4 % of the QTLs had a positive effect on the variation. Three of the seven QTLs, qRRM_3 , qRRF_1 , and qRRF_2 , were colocalized with markers IES43-5mt, IES68-6fs**, and IES108-1fs, respectively. Conclusions: To our knowledge, this is the first report on the construction of a genetic linkage map for purple sweetpotato (Jizishu 1) and the identification of QTLs associated with resistance to root rot in sweetpotato using SSR markers. These QTLs will have practical significance for the fine mapping of root rot resistance genes and play an important role in sweetpotato marker-assisted breeding.

scholarly journals Identification of QTL for resistance to root rot in sweetpotato (Ipomoea batatas (L.) Lam) with SSR linkage maps

2020 ◽  
Author(s):  
Zhimin Ma ◽  
Wenchuan Gao ◽  
Lanfu Liu ◽  
Minghui Liu ◽  
Ning Zhao ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Ssr Markers ◽  
Root Rot ◽  
Genetic Linkage ◽  
Practical Significance ◽  
Linkage Maps ◽  
Linkage Groups ◽  
Marker Distance ◽  
Average Marker Distance ◽  
Map Distance

Abstract Background: Sweetpotato root rot is a devastating disease caused by Fusarium solani that seriously endangers the yield of sweetpotato in China. 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 root rot have not yet been reported, and the biological mechanisms of resistance remain unclear in sweetpotato. Thus, increasing our knowledge about the mechanism of disease resistance and identifying resistance loci will assist in the development of disease resistance breeding. Results: In this study, we constructed genetic linkage maps of sweetpotato using a mapping population consisting of 300 individuals derived from a cross between Jizishu 1 and Longshu 9 by simple sequence repeat (SSR) markers, and mapped seven QTLs for resistance to root rot. In total, 484 and 573 polymorphic SSR markers were grouped into 90 linkage groups for Jizishu 1 and Longshu 9, respectively. The total map distance for Jizishu 1 was 3,974.24 cM, with an average marker distance of 8.23 cM. The total map distance for Longshu 9 was 5,163.35 cM, with an average marker distance of 9.01 cM. Five QTLs ( qRRM_1 , qRRM_2 , qRRM_3, qRRM_4 , and qRRM_5 ) were located in five linkage groups of Jizishu 1 map explaining 52.6–57.0% of the variation. Two QTLs ( qRRF_1 and qRRF_2 ) were mapped on two linkage groups of Longshu 9 explaining 57.6% and 53.6% of the variation, respectively. Furthermore, 71.4% of the QTLs positively affected the variation. Three of the seven QTLs, qRRM_3 , qRRF_1 , and qRRF_2 , were colocalized with markers IES43-5mt, IES68-6fs**, and IES108-1fs, respectively. Conclusions: To our knowledge, this is the first report on the construction of a genetic linkage map for purple sweetpotato (Jizishu 1) and the identification of QTLs associated with resistance to root rot in sweetpotato using SSR markers. These QTLs will have practical significance for the fine mapping of root rot resistance genes and play an important role in sweetpotato marker-assisted breeding.

scholarly journals Identification of QTL for resistance to root rot in sweetpotato (Ipomoea batatas (L.) Lam) with SSR linkage maps

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Zhimin Ma ◽  
Wenchuan Gao ◽  
Lanfu Liu ◽  
Minghui Liu ◽  
Ning Zhao ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Ssr Markers ◽  
Root Rot ◽  
Genetic Linkage ◽  
Practical Significance ◽  
Linkage Maps ◽  
Linkage Groups ◽  
Marker Distance ◽  
Average Marker Distance ◽  
Map Distance

Abstract Background Sweetpotato root rot is a devastating disease caused by Fusarium solani that seriously endangers the yield of sweetpotato in China. 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 root rot have not yet been reported, and the biological mechanisms of resistance remain unclear in sweetpotato. Thus, increasing our knowledge about the mechanism of disease resistance and identifying resistance loci will assist in the development of disease resistance breeding. Results In this study, we constructed genetic linkage maps of sweetpotato using a mapping population consisting of 300 individuals derived from a cross between Jizishu 1 and Longshu 9 by simple sequence repeat (SSR) markers, and mapped seven QTLs for resistance to root rot. In total, 484 and 573 polymorphic SSR markers were grouped into 90 linkage groups for Jizishu 1 and Longshu 9, respectively. The total map distance for Jizishu 1 was 3974.24 cM, with an average marker distance of 8.23 cM. The total map distance for Longshu 9 was 5163.35 cM, with an average marker distance of 9.01 cM. Five QTLs (qRRM_1, qRRM_2, qRRM_3, qRRM_4, and qRRM_5) were located in five linkage groups of Jizishu 1 map explaining 52.6–57.0% of the variation. Two QTLs (qRRF_1 and qRRF_2) were mapped on two linkage groups of Longshu 9 explaining 57.6 and 53.6% of the variation, respectively. Furthermore, 71.4% of the QTLs positively affected the variation. Three of the seven QTLs, qRRM_3, qRRF_1, and qRRF_2, were colocalized with markers IES43-5mt, IES68-6 fs**, and IES108-1 fs, respectively. Conclusions To our knowledge, this is the first report on the construction of a genetic linkage map for purple sweetpotato (Jizishu 1) and the identification of QTLs associated with resistance to root rot in sweetpotato using SSR markers. These QTLs will have practical significance for the fine mapping of root rot resistance genes and play an important role in sweetpotato marker-assisted breeding.

Two genetic linkage maps of mungbean using RFLP and RAPD markers

2000 ◽  
Vol 51 (4) ◽  
pp. 415 ◽  
Author(s):  
C. J. Lambrides ◽  
R. J. Lawn ◽  
I. D. Godwin ◽  
J. Manners ◽  
B. C. Imrie
Keyword(s):  
Linkage Map ◽  
Segregation Distortion ◽  
Recombinant Inbred ◽  
Genetic Linkage ◽  
Rapd Markers ◽  
Rflp Markers ◽  
Linkage Maps ◽  
Linkage Groups ◽  
Genetic Linkage Maps ◽  
Map Distance

Two genetic linkage maps of mungbean derived from the cross Berken ACC 41 are reported. The F2 map constructed from 67 individuals consisted of 110 markers (52 RFLP and 56 RAPD) that grouped into 12 linkage groups. The linked markers spanned a total map distance of 758.3 cM. A recombinant inbred (RI) population derived from the 67 F2 individuals was used for the generation of an additional linkage map. The RI map, composed entirely of RAPD markers, consisted of 115 markers in 12 linkage groups. The linked markers spanned a total map distance of 691.7 cM. Using a framework set of RFLP markers, the F2 map was compared with another F2 mungbean map constructed in Minnesota. In general, the order of these markers was consistent between maps. Segregation distortion was observed for some markers. 14.5% (16/110) of mapped F2 markers and 24% (28/115) of mapped RI markers segregated with distorted ratios. Segregation distortion occurred in each successive generation after the F2 . The regions of distortion identified in the Australian maps did not coincide with regions of the Minnesota map.

Targetting microsatellites (SSRs) in genetic linkage maps of bread wheat

2001 ◽  
Vol 52 (12) ◽  
pp. 1143 ◽  
Author(s):  
M. J. Hayden ◽  
S. Khatkar ◽  
P. J. Sharp
Keyword(s):  
Bread Wheat ◽  
Ssr Markers ◽  
Genetic Linkage ◽  
Linkage Maps ◽  
Linkage Groups ◽  
Intraspecific Polymorphism ◽  
Chromosomal Origin ◽  
Genetic Linkage Maps ◽  
Genomic Regions ◽  
Simple Sequence

The construction of genetic linkage maps from intraspecific crosses of bread wheat is slow and difficult due to very limited levels of polymorphism, which hinder the assignment of linkage groups to chromosomes and leave large genomic regions without markers. Simple sequence repeats (SSRs) reveal a higher incidence of polymorphism and are more informative than any other DNA marker, and are therefore considered a marker of choice for self-pollinating crops with little intraspecific polymorphism. However, the availability of SSRs in bread wheat is still limited. In this study, selectively amplified microsatellite (SAM) analysis was used to develop informative SSR markers to assist in the construction of an intraspecific wheat map. Three markers were developed for under-represented regions in the genetic map, and 7 for unassigned linkage groups. The latter SSRs permitted the chromosomal origin of 4 unassigned linkage groups to be determined. These results demonstrate the utility of SAM analysis for the targetted development of informative SSR markers to genomic regions of interest, and assignment of linkage groups to chromosomes. Furthermore, SAM analysis facilitates the development of markers for relatively short (<11) dinucleotide repeat sequences, a class of SSRs generally inaccessible to traditional hybridisation-based methods used to develop these markers.

Genetic Linkage Maps of the Guppy ( Poecilia reticulata ): Assignment of RAPD Markers to Multipoint Linkage Groups

2003 ◽  
Vol 5 (3) ◽  
pp. 279-293 ◽  
Author(s):  
Gideon Khoo ◽  
Meng Huat Lim ◽  
Haridas Suresh ◽  
Damien K. Y. Gan ◽  
Kok Fang Lim ◽  
...  
Keyword(s):  
Genetic Linkage ◽  
Rapd Markers ◽  
Poecilia Reticulata ◽  
Linkage Maps ◽  
Linkage Groups ◽  
Multipoint Linkage ◽  
Genetic Linkage Maps

A high-density genetic linkage map of a black spruce (Picea mariana) × red spruce (Picea rubens) interspecific hybrid

Genome ◽  
2011 ◽  
Vol 54 (2) ◽  
pp. 128-143 ◽  
Author(s):  
Bum-Yong Kang ◽  
John E. Major ◽  
Om P. Rajora
Keyword(s):  
Picea Mariana ◽  
Interspecific Hybrid ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Black Spruce ◽  
Picea Rubens ◽  
Red Spruce ◽  
Linkage Groups ◽  
Genomic Resource ◽  
Map Distance

Genetic maps provide an important genomic resource of basic and applied significance. Spruce ( Picea ) has a very large genome size (between 0.85 × 1010 and 2.4 × 1010 bp; 8.5–24.0 pg/1C, a mean of 17.7 pg/1C ). We have constructed a near-saturated genetic linkage map for an interspecific backcross (BC1) hybrid of black spruce (BS; Picea mariana (Mill.) B.S.P.) and red spruce (RS; Picea rubens Sarg.), using selectively amplified microsatellite polymorphic loci (SAMPL) markers. A total of 2284 SAMPL markers were resolved using 31 SAMPL–MseI selective nucleotide primer combinations. Of these, 1216 SAMPL markers showing Mendelian segregation were mapped, whereas 1068 (46.8%) SAMPL fragments showed segregation distortion at α = 0.05. Maternal, paternal, and consensus maps consistently coalesced into 12 linkage groups, corresponding to the haploid chromosome number (1n = 1x = 12) of 12 in the genus Picea. The maternal BS map consisted of 814 markers distributed over 12 linkage groups, covering 1670 cM, with a mean map distance of 2.1 cM between adjacent markers. The paternal BS × RS map consisted of 773 markers distributed over 12 linkage groups, covering 1563 cM, with a mean map distance of 2.0 cM between adjacent markers. The consensus interspecific hybrid BC1 map consisted of 1216 markers distributed over 12 linkage groups, covering 1865 cM (98% genome coverage), with a mean map distance of 1.5 cM between adjacent markers. The genetic map reported here provides an important genomic resource in Picea, Pinaceae, and conifers.

A genetic linkage map for Stevia rebaudiana

Genome ◽  
1999 ◽  
Vol 42 (4) ◽  
pp. 657-661 ◽  
Author(s):  
Y Yao ◽  
M Ban ◽  
J Brandle
Keyword(s):  
Linkage Map ◽  
Genetic Linkage ◽  
Rapd Markers ◽  
Genetic Linkage Map ◽  
Average Distance ◽  
Stevia Rebaudiana ◽  
Linkage Groups ◽  
Genome Map ◽  
High Level ◽  
Map Distance

To lay a foundation for molecular breeding efforts, the first genetic linkage map for Stevia rebaudiana has been constructed using segregation data from a pseudo test-cross F1 population. A total of 183 randomly amplified polymorphic DNA (RAPD) markers were analysed and assembled into 21 linkage groups covering a total distance of 1389 cM, with an average distance between markers of of 7.6 cM. The 11 largest linkage groups consisted of 4-19 loci, ranged in length from 56 to 174 cM, and accounted for 75% of the total map distance. Fifteen RAPD loci were found to be unlinked. From the 521 primers showing amplification products, 185 (35.5%) produced a total of 293 polymorphic fragments, indicating a high level of genetic diversity in stevia. Most of the RAPD markers in stevia segregated in normal Mendelian fashion.Key words: stevia, open-pollinated, genome map, RAPD.

scholarly journals Randomly Amplified Polymorphic DNA-based Genetic Linkage Maps of Three Apple Cultivars

1997 ◽  
Vol 122 (3) ◽  
pp. 350-359 ◽  
Author(s):  
Patrick J. Conner ◽  
Susan K. Brown ◽  
Norman F. Weeden
Keyword(s):  
Skin Color ◽  
Genetic Linkage ◽  
Average Distance ◽  
Scab Resistance ◽  
Linkage Maps ◽  
Randomly Amplified Polymorphic Dna ◽  
Linkage Groups ◽  
Single Linkage ◽  
Genetic Linkage Maps ◽  
Using Data

Genetic linkage maps were created for three apple (Malus ×domestica Borkh.) cultivars using data from two progenies (`Wijcik McIntosh' xNY 75441-67 and `Wijcik McIntosh' xNY 75441-58). The maps consist primarily of randomly amplified polymorphic DNA (RAPD) markers, but also contain six isozyme loci and four morphological markers (Rf, fruit skin color; Vf, scab resistance; Co, columnar growth habit; Ma, malic acid). Maps were constructed using a double pseudotestcross mapping format and JoinMap mapping software. An integrated `Wijcik McIntosh' map was produced by combining marker data from both progenies into a single linkage map. Homologous linkage groups from paternal maps were paired with their counterparts in the `Wijcik McIntosh' map using locus bridges composed of markers heterozygous in both parents of a progeny. The `Wijcik McIntosh' map consists of 238 markers arranged in 19 linkage groups spanning 1206 cM. The NY 75441-67 map contains 110 markers in 16 linkage groups and the NY 75441-58 map consists of 183 markers in 18 linkage groups. The average distance between markers in the maps was ≈5.0 cM.

Integration of the Cytogenetic and Genetic Linkage Maps of Brassica oleracea

Genetics ◽  
2002 ◽  
Vol 161 (3) ◽  
pp. 1225-1234 ◽  
Author(s):  
Elaine C Howell ◽  
Guy C Barker ◽  
Gareth H Jones ◽  
Michael J Kearsey ◽  
Graham J King ◽  
...  
Keyword(s):  
Linkage Map ◽  
Brassica Oleracea ◽  
Genetic Map ◽  
Genetic Linkage ◽  
Linkage Maps ◽  
Linkage Groups ◽  
Opposite Orientation ◽  
Cytogenetic Map ◽  
Specific Pcr ◽  
Genetic Linkage Maps

Abstract We have assigned all nine linkage groups of a Brassica oleracea genetic map to each of the nine chromosomes of the karyotype derived from mitotic metaphase spreads of the B. oleracea var. alboglabra line A12DHd using FISH. The majority of probes were BACs, with A12DHd DNA inserts, which give clear, reliable FISH signals. We have added nine markers to the existing integrated linkage map, distributed over six linkage groups. BACs were definitively assigned to linkage map positions through development of locus-specific PCR assays. Integration of the cytogenetic and genetic linkage maps was achieved with 22 probes representing 19 loci. Four chromosomes (2, 4, 7, and 9) are in the same orientation as their respective linkage groups (O4, O7, O8, and O6) whereas four chromosomes (1, 3, 5, and 8) and linkage groups (O3, O9, O2, and O1) are in the opposite orientation. The remaining chromosome (6) is probably in the opposite orientation. The cytogenetic map is an important resource for locating probes with unknown genetic map positions and is also being used to analyze the relationships between genetic and cytogenetic maps.

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