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

Abstract

Water yam (Dioscorea alata L.) is one of the most important food yams with wide geographical distribution in the tropics. One of the major constraints to water yam production is anthracnose disease caused by a fungus, Colletotrichum gloeosporioides (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. In a previous study, a total of 1,152 EST-SSRs were developed from >40,000 EST-sequences generated from two D. alata genotypes. A set of 380 EST-SSRs were validated as polymorphic when tested on two diverse parents targeted for anthracnose disease and were used to generate a saturated linkage map. Majority of the SSRs (60.2%) showed Mendelian segregation pattern and had no effect on the construction of linkage map. All 380 EST-SSRs were mapped into 20 linkage groups, and covered a total length of 3229.5 cM. Majority of the markers were mapped on linkage group 1 (LG 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. gloeosporioides from West Africa. Based on threshold LOD scores, one QTL was consistently observed on LG 14 in all the three years and average score data. This QTL was found at position interval of 71.1–84.8 cM explaining 68.5% 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 reference high-density genetic map of greater yam (Dioscorea alata L.)

“…It contains 20 linkage groups, as expected, and 1579 SNPs spread over 2613.5 cM, with an average marker interval of 1.7 cM. Indeed, using the same Kosambi mapping function, the previously published map lengths were 1233 cM, 1538 cM and 3229.5 cM, and they contained 494, 523 and 380 markers with an average marker spacing of 2.6 cM, 3.3 cM and 14.2 cM according to Mignouna et al (2002), Petro et al (2011) and Bhattacharjee et al (2018), respectively. The genome coverage was estimated at 65% by Mignouna et al (2002) and 80% by Petro et al (2011).…”

“…Then, the segregation distortion threshold excluded a higher proportion of markers in population B than in population A. Segregation distortions have been widely reported in plant species including D. alata . In Petro et al (2011), 19% of markers were tagged as distorted, while in Bhattacharjee et al (2018) it was 39.8%. However, comparisons are limited due to the unknown threshold used to test distortion.…”

“…(Terauchi and Konuma 1994; Misuki et al 2005; Tostain et al 2006; Hochu et al 2006; Andris et al 2010; Saski et al 2015). Moreover, an EST-SSR genetic linkage map containing 380 markers was recently published (Bhattacharjee et al 2018). Thus, the marker number is still limited for genome-wide approaches necessary for association genetics, and their implementation cost is relatively high.…”

Genome-Wide Identification and Evolutionary Analysis of NBS-LRR Genes From Dioscorea rotundata

“…This collectively contributes to the economic loss of the farmers. In the past, several studies have tried to collect germlines resistant to various pathogens and to map the resistance loci (Amusa, 2001;Mignouna et al, 2001Mignouna et al, , 2002Bhattacharjee et al, 2018). However, no functional disease resistance gene (R gene) has been cloned from yam crops so far.…”

Application of Efficient Express Sequence Tags Information for Classification and Functional Study of Simple Sequence Repeats in Cattle Testis Tissue

“…Usually, the expressed sequence tags (ESTs) containing SSRs located in the coding regions of genome are major concern in genetic studies because of their involvement in coding of amino acids and the functions of organs or tissues (Varshney et al, 2002). They may be applied in physical mapping techniques (Bhattacharjee et al, 2018), determination of gene expression (Ma et al, 2012), and sequence comparisons between normal and cancer tissues (Pu et al, 2013). The use of EST sequences has advantages such as the rapid identification of expressed genes, identification of gene families, phylogenetic analyses, survey of developmentally regulated genes, and examination of strain diversity (Li et al, 2003).…”