QTL underlying plant and first branch height in cassava (Manihot esculenta Crantz)
Research highlights
► Genetic linkage map of cassava was constructed based on SSR markers. ► QTL underlying plant height were identified. ► QTL underlying first branch height were identified.
Introduction
Cassava, Manihot esculenta Crantz subsp. Esculenta belongs to the Euphorbiaceae family (Raghu et al., 2007). It is a highly heterozygous crop plant because of out-crossing. The diploid state was 36 chromosomes (2n = 36) as described by Raghu et al. (2007). The haploid genome size was about 772 Mbp. Cultivated cassava was a perennial woody shrub cultivated for its starchy tuberous roots across the tropical and subtropical regions of the world. In Asia, South America and Africa, the cassava crop has been used as a major source of food for more than 500 million people (Daniell et al., 2008).
There are two types of propagation in cassava by either from asexually reproduced stem cuttings or by sexual reproduction with true seed (Alves, 2002). Propagation from true seed was a necessary strategy to generate new lines with high genetic diversity (Alves, 2002). About 5–6 years are needed from F1 hybrid seed germination of seed to the evaluation or selection stage. More time may be needed for the recurrent selection cycle if several locations have to be included (Kawano, 2003, Ceballos et al., 2004).
DNA markers can raise the rate and intensity of selection within breeding programs particularly for partial disease resistant genotypes and other traits of moderate heritability (Tyrka et al., 2008). Loci underlying important traits were identified by Quantitative Trait Loci (QTL) analysis and used in Marker-Assisted Selection programs (MAS). For cassava, the first genetic linkage map was constructed based on Restriction Fragment Length Polymorphism (RFLP) markers in an F1 mapping population and the second map was constructed based on Simple Sequence Repeats (SSR) markers using an F2 mapping population (Fregene et al., 1997, Okogbenin et al., 2006, Akinbo et al., 2007). In addition, two genetic linkage maps were constructed based on; Amplified Fragment Length Polymorphisms (AFLPs) and genomic SSRs (Kunkeaw et al., 2010); and both genomic SSRs and expressed sequence tag (EST)–SSRs (Kunkeaw et al., 2011). However, those maps have not been used for QTL analysis.
The economically important traits of crops include yield, quality and partial disease resistance. Like many agronomic traits, they were controlled by many genes (Ribaut and Hoisington, 1998, Collard et al., 2005). To develop high yield crop varieties, the relationships between yield, plant architecture, photosynthesis, leaf area and biomass partitioning have been investigated in many crops (Okogbenin and Fregene, 2003). Very tall plants were often vulnerable to lodging and so provided lower harvestable yield and lower quality grains (Ji-hua et al., 2007, Wei et al., 2009). Consequently, among genotypes selected for short stature plant height has been associated with high yield and high harvest index in many grain crop species (Zhang et al., 2006, Alcivar et al., 2007). Similar correlations have been made for root biomass crops like cassava which indicated that storage root yield was genetically related to the number of storage roots per plant, root size, harvest index, stem girth, canopy width and the total number of branches (reviewed by Ntawuruhunga and Dixon, 2009). In another root crop, potato (Solanum tuberosum) grown in tropical regions (Maity and Chatteriee, 1977), leaflet size had the maximum influence on yield followed by number of tubers/plant and plant height. Therefore, shoot morphology and architecture were important indicators of yield in several plant crops, including cassava. This study aimed to construct a genetic linkage map of cassava using an F1 mapping population and identify QTL underlying plant and first branch height at different locations and over time. The information found in this study should be useful for breeding selection in cassava in the future.
Section snippets
Plant materials
A total of 100 progeny that segregated from an F1 mapping population were used. They derived from a cross between cassava varieties ‘Huaybong60’ as the female parent and ‘Hanatee’ as the male parent. The population was grown at the Rayong Field Crops Research Center, Department of Agriculture, in central Thailand in years 2007–2009 and at the Lopburi Field Crops Research Center, Department of Agriculture, Thailand in 2009. Additionally, the population grown in the year 2009 at both locations
Phenotype analysis
For the F1 mapping populations, the calculations of means, minimum and maximum values, standard deviations, skewness and kurtosis were summarized in Table 1. Plant heights ranged from 111.5 to 382.7 cm. First branch heights ranged from 40 to 280 cm. All traits were approximately normal, which inferred the traits were polygenic (or quantitative). Skewness was less than 0.74 and more than −0.48, peaking (Kurtosis) was within 0.12 to −0.98. Correlations among the plant height and first branch height
Discussion
Okogbenin et al. (2006) had reported that a high level of segregation distortion was commonly found in out-crossing species. However, the amount of markers that showed segregation distortion detected in this study (23.4%) were slightly lower than detected in the earlier study (27.0%). The map consisted of 25 linkage groups rather than 18 the number of haploid chromosomes (Sun et al., 2008). However, three of the linkage groups had only two markers and four linkage groups had only three markers.
Conclusion
This study has constructed SSR-based genetic linkage map of an F1 mapping population derived from cross between Huaybong60 and Hanatee. The map was applied for identification of QTL underlying plant and first branch height. QTL explaining large portions of the phenotypic variance were identified in this study, supporting the hypothesis that these two traits were controlled by several genes or loci with large effects. However, QTL were all location and year specific. The QTL underlying plant and
Acknowledgements
This research was supported by National Center for Genetic Engineering and Biotechnology (Thailand), Commission on Higher Education, Ministry of Education (Thailand), the Thailand Research Fund and Mahidol University. SS and AB were supported from Thailand Graduate Institute of Science and Technology (TGIST) for Ph.D. and M.S. studies, respectively. Financial support from the Thailand Research Fund through the Royal Golden Jubilee Ph.D. Program to (Grant No. PHD 4LMU/52/W1) AB and KT is
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