A genome scan for quantitative trait loci affecting cyanogenic potential of cassava root in an outbred population

Abstract

BackgroundCassava (Manihot esculenta Crantz) can produce cyanide, a toxic compound, without self-injury. That ability was called the cyanogenic potential (CN). This project aimed to identify quantitative trait loci (QTL) associated with the CN in an outbred population derived from 'Hanatee' × 'Huay Bong 60', two contrasting cultivars. CN was evaluated in 2008 and in 2009 at Rayong province, and in 2009 at Lop Buri province, Thailand. CN was measured using a picrate paper kit. QTL analysis affecting CN was performed with 303 SSR markers.ResultsThe phenotypic values showed continuous variation with transgressive segregation events with more (115 ppm) and less CN (15 ppm) than either parent ('Hanatee' had 33 ppm and 'Huay Bong 60' had 95 ppm). The linkage map consisted of 303 SSR markers, on 27 linkage groups with a map that encompassed 1,328 cM. The average marker interval was 5.8 cM. Five QTL underlying CN were detected. CN08R1from 2008 at Rayong, CN09R1and CN09R2 from 2009 at Rayong, and CN09L1 and CN09L2 from 2009 at Lop Buri were mapped on linkage group 2, 5, 10 and 11, respectively. Among all the identified QTL, CN09R1 was the most significantly associated with the CN trait with LOD score 5.75 and explained the greatest percentage of phenotypic variation (%Expl.) of 26%.ConclusionsFive new QTL affecting CN were successfully identified from 4 linkage groups. Discovery of these QTL can provide useful markers to assist in cassava breeding and studying genes affecting the trait.

Validation of a reference gene for transcript analysis in cassava (Manihot esculenta Crantz) and its application in analysis of linamarase and -hydroxynitrile lyase expression at different growth stages

“…The efficiency of amplification of all primer pairs ranged from 95-105% and r 2 >0.99, which is in accordance with established criteria for real-time RT-PCR (Bio-Rad Laboratories, 2006; Dhami and Kumarasinghe, 2014;Ma et al, 2013). In order to determine the most stable reference genes, expression levels of transcripts from these six reference genes were determined in Huay Bong 60 and Hanatee, which are significantly different in CN (Whankaew et al, 2011) at 6, 9 and 12 MAP. Stability of the reference genes according to the NormFinder software are shown in Figure 1.…”

“…Cassava varieties Huay Bong 60 (high CN), Hanatee (low CN), and five low and five high CN plants from a previously described F1 mapping population (Whankaew et al, 2011) were grown at the Rayong Field Crops Research Center, Department of Agriculture, Thailand. Cassava leaves and roots were collected at 6, 9, and 12 month after planting (MAP), then snap frozen in liquid nitrogen until RNA isolation.…”

“…The expression profiles of these genes were analyzed in six plants each of low and high CN, consisting of the parental Huay Bong 60 and Hanatee and an additional five plants with low CN and five with high CN from a previously described F1 mapping population (Whankaew et al, 2011). Expression of LNM and HNL was extremely low in root samples, with correspondingly high Ct values, and so expression analysis is only presented for leaf samples.…”

Cassava traits and end-user preference: Relating traits to consumer liking, sensory perception, and genetics

“…Several studies have looked at the genetic mapping of cyanide related genes (Balyejusa Kizito et al, 2007;Whankaew et al, 2011).…”

“…It appears that one QTL for CNP and one QTL for dry matter content mapped near each other, suggesting pleiotrophy and/or linkage for both traits. Whankaew et al, 2011 working with low and high cyanide cultivars also identifying QTL responsible for cyanide (CN):…”