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

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.

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

PLoS ONE ◽  
2018 ◽  
Vol 13 (10) ◽  
pp. e0197717 ◽  
Author(s):  
Ranjana Bhattacharjee ◽  
Christian O. Nwadili ◽  
Christopher A. Saski ◽  
Agre Paterne ◽  
Brian E. Scheffler ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Linkage Map ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Dioscorea Alata ◽  
Anthracnose Disease ◽  
Water Yam

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

2018 ◽  
Author(s):  
Ranjana Bhattacharjee ◽  
Christian O Nwadili ◽  
Christopher A Saski ◽  
Agre Paterne ◽  
Brian E. Scheffler ◽  
...  
Keyword(s):  
Linkage Map ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Average Score ◽  
Dioscorea Alata ◽  
Marker Density ◽  
Linkage Groups ◽  
Anthracnose Disease ◽  
High Marker Density ◽  
Water Yam

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.

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

2002 ◽  
Vol 105 (5) ◽  
pp. 726-735 ◽  
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

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 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 High-density Mapping for Gray Leaf Spot Resistance using Two Related Tropical Maize RIL Populations

2021 ◽  
Author(s):  
Long Chen ◽  
Li Liu ◽  
Ziwei Li ◽  
Yudong Zhang ◽  
Manjit S Kang ◽  
...  
Keyword(s):  
Leaf Spot ◽  
Large Scale ◽  
Gene Annotation ◽  
Snp Markers ◽  
Gray Leaf Spot ◽  
High Density ◽  
Genetic Maps ◽  
Phenotypic Variance ◽  
Maize Breeding ◽  
Density Mapping

Abstract The identification of QTL/genes to resist gray leaf spot (GLS) caused by Cercospora zeae-maydis or Cercospora Zeina plays an urgent role in improving GLS resistance in maize breeding practice. In our study, two groups of recombinant inbred line (RIL) populations derived from CML373×Ye107 (176 RILs) and Chang7-2×Ye107 (190 RILs) were generated and subjected to genotyping-by-sequencing (GBS). GBS technology was used for large-scale single nucleotide polymorphism (SNP) discovery and simultaneous genotyping of all F7 lines from two related RIL populations in order to identify quantitative trait loci (QTL) associated with GLS resistance under natural conditions of disease occurrence. A total of 1929222287 reads in CML373×Ye107 (RIL-YCML) and 2585728312 reads in Chang7-2×Ye107 (RIL-YChang), with an average of 10961490 (RIL-YCML) and 13609096 (RIL-YChang) reads per individual, were got, which was roughly equal to 0.70-fold and 0.87-fold coverage of the maize B73 RefGen_V4 genome for each F7 individual, respectively. 6418 and 5139 SNP markers were extracted to construct two high-density genetic maps. Comparative analysis using these physically mapped marker loci demonstrated a satisfactory colinear relationship with the reference genome. Eleven GLS-resistant QTL have been detected. The individual QTL accounted for 2.05-24.00% of the phenotypic variance explained (PVE). The new consensus QTL (qYCM-DS3-3/ qYCM-LT3-1/ qYCM-LT3-2) with the largest effect was located in chromosome bin 3.05, with an interval of 2.7 Mb, representing 13.08 to 24.00% of the PVE. Further gene annotation indicated that there were four candidate genes (GRMZM2G032384, GRMZM2G041415, GRMZM2G041544, and GRMZM2G035992) for qYCM-LT3-1, which may be related to GLS resistance.

scholarly journals Development of High-Density Genetic Linkage Maps and Identification of Loci for Chestnut Gall Wasp Resistance in Castanea spp.

Plants ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 1048
Author(s):  
Daniela Torello Marinoni ◽  
Sogo Nishio ◽  
Nadia Valentini ◽  
Kenta Shirasawa ◽  
Alberto Acquadro ◽  
...  
Keyword(s):  
Genetic Linkage ◽  
Castanea Sativa ◽  
High Density ◽  
Genetic Maps ◽  
Phenotypic Variance ◽  
Linkage Maps ◽  
Gall Wasp ◽  
Resistance Response ◽  
Genetic Linkage Maps ◽  
Resistance Trait

Castanea sativa is an important multipurpose species in Europe for nut and timber production as well as for its role in the landscape and in the forest ecosystem. This species has low tolerance to chestnut gall wasp (Dryocosmus kuriphilus Yasumatsu), which is a pest that was accidentally introduced into Europe in early 2000 and devastated forest and orchard trees. Resistance to the gall wasp was found in the hybrid cultivar ‘Bouche de Bétizac’ (C. sativa × C. crenata) and studied by developing genetic linkage maps using a population derived from a cross between ‘Bouche de Bétizac’ and the susceptible cultivar ‘Madonna’ (C. sativa). The high-density genetic maps were constructed using double-digest restriction site-associated DNA-seq and simple sequence repeat markers. The map of ‘Bouche de Bétizac’ consisted of 1459 loci and spanned 809.6 cM; the map of ‘Madonna’ consisted of 1089 loci and spanned 753.3 cM. In both maps, 12 linkage groups were identified. A single major QTL was recognized on the ‘Bouche de Bétizac’ map, explaining up to 67–69% of the phenotypic variance of the resistance trait (Rdk1). The Rdk1 quantitative trait loci (QTL) region included 11 scaffolds and two candidate genes putatively involved in the resistance response were identified. This study will contribute to C. sativa breeding programs and to the study of Rdk1 genes.

scholarly journals Chromosome Level Assembly of Homozygous Inbred Line ‘Wongyo 3115’ Facilitates the Construction of a High-Density Linkage Map and Identification of QTLs Associated With Fruit Firmness in Octoploid Strawberry (Fragaria × ananassa)

2021 ◽  
Vol 12 ◽  
Author(s):  
Hye-Eun Lee ◽  
Abinaya Manivannan ◽  
Sun Yi Lee ◽  
Koeun Han ◽  
Jun-Geol Yeum ◽  
...  
Keyword(s):  
Linkage Map ◽  
Inbred Line ◽  
High Density ◽  
Genetic Maps ◽  
Fruit Firmness ◽  
Sequencing Technologies ◽  
A Genome ◽  
Genetic Mechanisms ◽  
Trait Locus ◽  
Chromosome Level

Strawberry is an allo-octoploid crop with high genome heterozygosity and complexity, which hinders the sequencing and the assembly of the genome. However, in the present study, we have generated a chromosome level assembly of octoploid strawberry sourced from a highly homozygous inbred line ‘Wongyo 3115’, using long- and short-read sequencing technologies. The assembly of ‘Wongyo 3115’ produced 805.6 Mb of the genome with 323 contigs scaffolded into 208 scaffolds with an N50 of 27.3 Mb after further gap filling. The whole genome annotation resulted in 151,892 genes with a gene density of 188.52 (genes/Mb) and validation of a genome, using BUSCO analysis resulted in 94.10% complete BUSCOs. Firmness is one of the vital traits in strawberry, which facilitate the postharvest shelf-life qualities. The molecular and genetic mechanisms that contribute the firmness in strawberry remain unclear. We have constructed a high-density genetic map based on the ‘Wongyo 3115’ reference genome to identify loci associated with firmness in the present study. For the quantitative trait locus (QTL) identification, the ‘BS F2’ populations developed from two inbred lines were genotyped, using an Axiom 35K strawberry chip, and marker positions were analyzed based on the ‘Wongyo 3115’ genome. Genetic maps were constructed with 1,049 bin markers, spanning the 3,861 cM. Using firmness data of ‘BS F2’ obtained from 2 consecutive years, five QTLs were identified on chromosomes 3-3, 5-1, 6-1, and 6-4. Furthermore, we predicted the candidate genes associated with firmness in strawberries by utilizing transcriptome data and QTL information. Overall, we present the chromosome-level assembly and annotation of a homozygous octoploid strawberry inbred line and a linkage map constructed to identify QTLs associated with fruit firmness.

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