Yam (Dioscorea spp.) is a multi-species monocotyledonous crop widely grown in the tropics and subtropics . It is the most valuable crop in West Africa, where its cultivation began 11,000 years ago . Of the over 600 yam species, water yam (D. alata) is the extensively cultivated species worldwide . In Africa, white yam (D. rotundata) is the most cultivated yam species followed by water yam . In West Africa, yam production is mainly by smallholder farmers, making it a major source of farm employment and income for this group. In addition, yam plays significant role in traditional medicine and in the socio-cultural life of the people as it is involved in many key life ceremonies .
Water yam possess a number of valuable attributes for cultivation and consumption. These include high multiplication ratio, early vigour for weed smothering, higher genetic potential for high yield (especially under low to average soil fertility), low post-harvest losses, good processing quality and high nutritive value including its possession of low glycemic index [5; 6]. However, anthracnose disease caused by the Colletotrichum gloeosporioides (Penz) is the most limiting factor affecting productivity of water yam in many regions of the world . Anthracnose causes mild to acute leaf necrosis, premature leaf abscission and shoot die-back . Severe infections result in defoliation leaving naked, black and drying vines . Yield losses from the disease of up to 90% have been reported under severe conditions on different cultivars of water yam in West Africa, Central America and the Pacific [10, 11, 12, 13]. High genetic and pathogenic variance has been reported among isolates of C. gloeosporioides from different geographical locations [7, 14, 15], suggesting that there is high probability for the geographic variation in strains, some of which could overcome existing resistance .
Cultural control approaches such as the use of disease-free planting materials, adjustment of plant spacing and planting dates, burying infected plant residues in the soil immediately after harvesting, intercropping, crop rotation with non-host crops and fallowing have been used in other plant pathosystems to reduce pathogen inoculum in the field, delay disease onset, or slow disease progress [17, 18]. Nonetheless, these disease management practices have not been effective for controlling anthracnose disease in water yam or result in substantial increase in tuber yield , especially in disease endemic areas. Also, biological control to impede or outcompete the multiplication and spread of virulent C. gloeosporioides strains in yam fields has been limited . Chemical control can be an effective disease management approach but most yam producers are smallholder growers and may not have the prerequisite technical support and finance to afford the use of fungicides . Furthermore, inappropriate use of fungicides could potentially result in the development of resistant C. gloeosporioides strains to systemic fungicides  as well as detrimental environmental effects. The best control option is therefore the development and deployment of anthracnose resistant water yam varieties. It is, therefore, expedient to develop varieties with multiple disease resistance genes to provide stable and durable resistance against the broad spectrum of the fungal pathogen.
Substantial progress has been made to develop anthracnose resistant water yam varieties at the International Institute of Tropical Agriculture (IITA), Nigeria and national agricultural research systems in West Africa and elsewhere through conventional breeding using phenotypic observations. This effort is, however, arduous and considerably slow due to the inherent biological constraints of a heterozygous vegetatively propagated crop . Genomics-informed breeding techniques such as molecular marker assisted breeding and genomic selection would accelerate efforts in introgresssing anthracnose resistance into preferred genetic backgrounds .
Earlier investigations on anthracnose disease in water yam showed that resistance is likely to be dominant and quantitatively inherited . Efforts have also been made to identify QTL controlling YAD using low-throughput molecular markers and less dense or unsaturated genetic maps such as AFLP markers [5, 25] and EST-SSRs . Prospects for locating additional QTL and applying molecular breeding methods in water yam improvement programs is very promising especially due to advances in next-generation sequencing and the recent development of the reference genome sequence of D. rotundata and D. alata. The objective of this study was to develop a SNP-based genetic linkage map and identify QTL for anthracnose disease resistance in a bi-parental mapping population of D. alata.