An EST-SSR based genetic linkage map and identification of QTLs for anthracnose disease resistance in water yam (Dioscorea alata L.)

AbstractWater yam (Dioscorea alata L.) is one of the most important food yams with wide geographical distribution in tropics. One of the major constraints to water yam production is anthracnose disease caused by a fungus, Colletotrichum gloesporioides (Penz.). There are no economically feasible solutions as chemical sprays or cultural practices, such as crop rotation are seldom convenient for smallholder farmers for sustainable control of the disease. Breeding for development of durable genetic resistant varieties is known to offer lasting solution to control endemic disease threats to crop production. However, breeding for resistance to anthracnose has been slow considering the biological constraints related to the heterozygous and vegetative propagation of the crop. The development of saturated linkage maps with high marker density, such as SSRs, followed by identification of QTLs can accelerate the speed and precision of resistance breeding in water yam. A total of 380 EST-SSRs were used to generate a saturated linkage map. About 60.19% of SSRs showed Mendelian segregation pattern, however, it had no effect on the construction of linkage map. All 380 EST-SSRs were mapped into 20 linkage groups covering a total length of 2559.66 cM, which agrees with the diploid nature (2n = 2x = 20) of the parents used in the cross. Majority of the markers were mapped on linkage group 1 comprising of 97 EST-SSRs. This is the first genetic linkage map of water yam constructed using EST-SSRs. QTL localization was based on phenotypic data collected over a 3-year period of inoculating the mapping population with the most virulent strain of C. gloeosporoides from West Africa. Using the mean permutation value of LOD scores as threshold value for declaring a putative QTL on all linkage groups, one QTL was consistently observed on linkage group (LG) 14 in all the three years and average score data. This QTL was found at position interval of 71.12 – 84.76 cM explaining 68.94% of the total phenotypic variation in the average score data. The high marker density allowed identification of QTLs and association for anthracnose disease, which could be validated in other mapping populations and used in marker-assisted breeding in D. alata improvement programmes.

Download Full-text

A SNP-Based Linkage Map and QTL Identification for Resistance to Yam Anthracnose Disease (YAD) in Water Yam (Dioscorea alata)

10.21203/rs.3.rs-26806/v1 ◽

2020 ◽

Author(s):

Kwabena Darkwa ◽

Paterne AGRE ◽

Bunmi Olasanmi ◽

Olufisayo Kolade ◽

Pierre Mournet ◽

...

Keyword(s):

Disease Resistance ◽

Linkage Map ◽

High Density ◽

Genetic Maps ◽

Dioscorea Alata ◽

Valuable Insight ◽

Phenotypic Variance ◽

Anthracnose Resistance ◽

Anthracnose Disease ◽

Water Yam

Abstract Background: Yam anthracnose disease (YAD) caused by Colletotrichum gloeosporioides is the primary cause of yield loss in water yam (Dioscorea alata), the widely cultivated species of yam. Development of resistant cultivars have been a prime target for sustainable management of anthracnose in water yam. Molecular breeding tools are required to expedite the development of improved yam varieties. QTL analysis using high density genetic maps serve as a powerful tool to discover key locations of quantitave traits. This study aimed at tagging quantitative trait loci (QTL) for anthracnose disease resistance in a bi-parental mapping population of D. alata.Results: In this study, two contrasting parents for yam anthracnose disease reaction and their 204 full- sib offspring were used to develop a high-density genetic linkage map with 3,257 SNP markers by the GBS technique. The total length of the consensus map was 1460.94 cM with an average of 163 markers per chromosome. Four QTLs were detected for anthracnose disease resistance in 4 locations on 3 chromosomes. The proportion of phenotypic variance explained by these QTLs ranged from 10 to 13%. Plant defense response genes including GDSL-like Lipase/Acylhydrolase, Protein kinase domain and F-box protein were also detected within the QTL regions. Conclusion: The results from the present study provide valuable insight into the genetic architecture of anthracnose resistance in water yam. The candidate markers and putative genes identified herewith form a relevant resource to apply marker-assisted selection as alternative to a conventional labor-intensive screening for anthracnose resistance in water yam.

Download Full-text

A genetic linkage map of water yam (Dioscorea alata L.) based on AFLP markers and QTL analysis for anthracnose resistance

Theoretical and Applied Genetics ◽

10.1007/s00122-002-0912-6 ◽

2002 ◽

Vol 105 (5) ◽

pp. 726-735 ◽

Cited By ~ 41

Author(s):

H. Mignouna ◽

R. Mank ◽

T. Ellis ◽

N. van den Bosch ◽

R. Asiedu ◽

...

Keyword(s):

Linkage Map ◽

Qtl Analysis ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Aflp Markers ◽

Dioscorea Alata ◽

Anthracnose Resistance ◽

Water Yam

Download Full-text

Mapping of quantitative trait loci underlying resistance to cassava anthracnose disease

The Journal of Agricultural Science ◽

10.1017/s0021859615001057 ◽

2015 ◽

Vol 154 (7) ◽

pp. 1209-1217 ◽

Cited By ~ 3

Author(s):

A. BOONCHANAWIWAT ◽

S. SRAPHET ◽

S. WHANKAEW ◽

O. BOONSENG ◽

D. R. SMITH ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Linkage Map ◽

Dna Markers ◽

Quantitative Trait ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Gene Annotation ◽

Linkage Groups ◽

Anthracnose Disease ◽

Trait Loci

SUMMARYCassava (Manihot esculenta Crantz) is an economically important root crop in Thailand, which is ranked the world's top cassava exporting country. Production of cassava can be hampered by several pathogens and pests. Cassava anthracnose disease (CAD) is an important disease caused by the fungus Colletotrichum gloeosporioides f. sp. manihotis. The pathogen causes severe stem damage resulting in yield reductions and lack of stem cuttings available for planting. Molecular studies of cassava response to CAD will provide useful information for cassava breeders to develop new varieties with resistance to the disease. The current study aimed to identify quantitative trait loci (QTL) and DNA markers associated with resistance to CAD. A total of 200 lines of two F1 mapping populations were generated by reciprocal crosses between the varieties Huabong60 and Hanatee. The F1 samples were genotyped based on simple sequence repeat (SSR) and expressed sequence tag-SSR markers and a genetic linkage map was constructed using the JoinMap®/version3·0 program. The results showed that the map consisted of 512 marker loci distributed on 24 linkage groups with a map length of 1771·9 centimorgan (cM) and a mean interval between markers of 5·7 cM. The genetic linkage map was integrated with phenotypic data for the response to CAD infection generated by a detached leaf assay test. A total of three QTL underlying the trait were identified on three linkage groups using the MapQTL®/version4·0 program. Those DNA markers linked to the QTL that showed high statistically significant values with the CAD resistance trait were identified for gene annotation analysis and 23 candidate resistance genes to CAD infection were identified.

Download Full-text

Development of a genetic linkage map for Pinus radiata and detection of pitch canker disease resistance associated QTLs

Trees ◽

10.1007/s00468-014-1090-2 ◽

2014 ◽

Vol 28 (6) ◽

pp. 1823-1835 ◽

Cited By ~ 10

Author(s):

P. Moraga-Suazo ◽

L. Orellana ◽

P. Quiroga ◽

C. Balocchi ◽

E. Sanfuentes ◽

...

Keyword(s):

Disease Resistance ◽

Linkage Map ◽

Pinus Radiata ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Pitch Canker ◽

Canker Disease

Download Full-text

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

Frontiers in Plant Science ◽

10.3389/fpls.2021.671620 ◽

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.

Download Full-text

First genetic linkage map of Lathyrus cicera based on RNA sequencing-derived markers: Key tool for genetic mapping of disease resistance

Horticulture Research ◽

10.1038/s41438-018-0047-9 ◽

2018 ◽

Vol 5 (1) ◽

Cited By ~ 2

Author(s):

Carmen Santos ◽

Nuno Felipe Almeida ◽

Mara Lisa Alves ◽

Ralf Horres ◽

Nicolas Krezdorn ◽

...

Keyword(s):

Disease Resistance ◽

Genetic Mapping ◽

Linkage Map ◽

Rna Sequencing ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Lathyrus Cicera

Download Full-text

Genetic Basis of Cyprinid Herpes Virus-3 Resistance in Common Carp

10.32747/2011.7592645.bard ◽

2011 ◽

Author(s):

Lior David ◽

Yaniv Palti ◽

Moshe Kotler ◽

Gideon Hulata ◽

Eric M. Hallerman

Keyword(s):

Disease Resistance ◽

Linkage Map ◽

Common Carp ◽

Genetic Linkage ◽

Herpes Virus ◽

Genetic Linkage Map ◽

Viral Disease ◽

Economic Damage ◽

Wild Type ◽

Herpès Virus

The goal of this project was to provide scientific and technical basis for initiating the development of breeding protocols using marker assisted selection for viral disease resistance in common carp. The specific objectives were: 1) Establishing families and characterizing the phenotypic and genetic variation of viral resistance; 2) Measuring the dynamics of immune response and developing a method to measure the long term immune memory; 3) Developing markers and generating a new genetic linkage map, which will enable initial QTL mapping; and, 4) Identifying genetic linkage of markers and candidate genes (like MHC and TLRs) with resistance to CyHV-3. The common carp is an important farmed freshwater fish species in the world. Edible carp is second only to tilapia in Israeli aquaculture production and ornamental carp (koi) is an important product in both the US and Israel. Carp industries worldwide have recently suffered enormous economic damage due to a viral disease caused by Cyprinid herpes virus 3 (CyHV-3). Aside from preventative measures, a sustainable solution to this problem will be to establish a genetic improvement program of the resistance of fish to the pathogen. The aims of the project was to take the necessary first steps towards that. The differences in survival rates after infection with CyHV-3 virus among 20 families from six types of crosses between three carp lines (two commercial lines and one wild-type carp) revealed that the wild-type carp and its crosses had a much-improved survival over the crosses of the commercial lines themselves. These crosses set the starting point for breeding of commercial strains with improved resistance. Resistant fish had lower antibody titer against the virus suggesting that resistance might depend more on the innate immunity. A set of 500 microsateliite markers was developed and the markers are currently being used for generating a genetic linkage map for carp and for identifying disease resistance QTL. Fourteen candidate immune genes, some of which were duplicated, were cloned from the carp and SNP markers were identified in them. The expression of these genes varied between tissues and suggested functional divergence of some duplicated genes. Initial association between CyHV-3 resistance and one of the genes was found when SNP alleles in these genes were tested for their segregation between susceptible and resistant progeny. The results of this project have implications to the development of viral resistant commercial carp strains and effective immunization against this aggressive disease. The genetic and immunological knowledge accumulated in this project will not only promote carp and koi production but will also contribute to a broader understanding of fish immunogenetics.

Download Full-text