Simple sequence repeat (SSR) markers provide a powerful tool for genetic linkage map construction that can be applied for identification of quantitative trait loci (QTL). In this study, a total of 640 new SSR markers were developed from an enriched genomic DNA library of the cassava variety 'Huay Bong 60' and 1,500 novel expressed sequence tag-simple sequence repeat (EST-SSR) loci were developed from the Genbank database. To construct a genetic linkage map of cassava, a 100 F(1) line mapping population was developed from the cross Huay Bong 60 by 'Hanatee'. Polymorphism screening between the parental lines revealed that 199 SSRs and 168 EST-SSRs were identified as novel polymorphic markers. Combining with previously developed SSRs, we report a linkage map consisted of 510 markers encompassing 1,420.3 cM, distributed on 23 linkage groups with a mean distance between markers of 4.54 cM. Comparison analysis of the SSR order on the cassava linkage map and the cassava genome sequences allowed us to locate 284 scaffolds on the genetic map. Although the number of linkage groups reported here revealed that this F(1) genetic linkage map is not yet a saturated map, it encompassed around 88% of the cassava genome indicating that the map was almost complete. Therefore, sufficient markers now exist to encompass most of the genomes and efficiently map traits in cassava.

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SUMMARYCassava (Manihot esculenta Crantz) root yield measured as fresh weight (hereafter root yield) is declining in much of Asia and Africa. The current study aimed to identify quantitative trait loci (QTL) underlying both root and starch fresh weights in F1 cassava. Eight QTL were associated with root yield, underlying 12·9–40·0% of the phenotypic variation (PVE). Nine QTL were associated with starch content, underlying 11·3–27·3% of the PVE. Quantitative trait loci were identified from four different environments that encompassed two locations and 3 years. Consistent QTL for root yield, YLD5_R11 and YLD8_L09 on linkage group (LG) 16, were detected across years and locations. Quantitative trait loci for starch content, ST3_R09, ST6_R10 and ST7_R11 on LG 11, were found across 3 years. Co-localization of QTL for both traits with positive correlation was detected between YLD3_R10 and ST5_R10 on LG 9. Candidate genes within the QTL that were consistent across multiple environments were identified based on cassava genome sequences. Genes predicted to encode for glycosyl hydrolases, uridine 5’-diphospho-(UDP)-glucuronosyl transferases and UDP-glucosyl transferases were found among the 44 genes located within the region containing the QTL controlling starch content. Sixteen genes predicted to encode proteins that were possibly associated with root yield were identified. The QTL controlling root yield and starch content in the current study will be useful for molecular breeding of cassava through marker-assisted selection. The identification of candidate genes underlying both traits will be useful both as markers and for gene expression studies.

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.