Abstract
Cassava (Manihot esculenta Crantz) is an important tropical starchy root crop that is adapted to drought but extremely cold sensitive. A cold-tolerant, high-quality, and robust supply of cassava is urgently needed. Here, we clarify genome-wide distribution and classification of CCGG hemi-methylation and full-methylation, and detected 77 much candidate QTLsepi for cold stress and 103 much candidate QTLsepi for storage root quality and yield in 186 cassava population, generated by crossing two non-inbred lines with female parent KU50 and male parent SC124 (KS population). We developed amplified-fragment single nucleotide polymorphism and methylation (AFSM) genetic map in this population. We also constructed the AFSM QTL map, identified 260 much candidate QTL genes for cold stress and 301 much candidate QTL genes for storage root quality and yield, based on the years greenhouse and field trials. This may accounted for a significant amount of the variation in the key traits controlling cold tolerance and the high quality and yield of cassava.
Highlights
The majority of studies on many species are based on the complex traits[1,2,3]
We found 318 methylated quantitative trait loci (QTL) genes that were significantly associated with cold tolerance (CT-QTLGsepi, including 11 repeatable CT-QTLGsepi) and 524 that were significantly associated with quality and yield (QY-QTLGsepi, including 105 repeatable QY-QTLGsepi), based on the correlation analysis (x2 test, p < 0.01, Fig. 3 and Table S5)
In accordance with previous studies showed that mitogen-activated protein kinase kinase 4 (MKK4) were activated and rising its mRNA levels by cold stress in a mitogen-activated protein kinase pathway, suggested it could be a plant stress signaling[24], we found MKK4 (Mes.gk046937) was significantly associated with Relative storage root yield (rSRY)-2 (Fig. S7e)
Summary
The majority of studies on many species are based on the complex traits[1,2,3]. Even though an increasing number of studies are investigating the heritable phenotypic variation in the model plants, such as Arabidopsis thaliana[2,4,5] and soybean[6], the heritable variations in cytosine methylation in non-model crops have not been investigated[7,8]. A key challenge in the field of population genetics is showing the changes in the genome-wide CCGG hemi-methylation and full-methylation heritable variation patterns and SNVs (single-nucleotide polymorphisms and indels) associated with heritable phenotypic variation in populations with high heterozygosity and large genomes To address these difficulties, we established in a cassava population with a highly heterozygous and large genome[13], and measured eight complex traits through field and greenhouse experiments. Cassavas from the KS population and performed deep sequencing on the transcriptomes of the parents to assess the function of the differentially methylated regions (DMRs), and to clarify the relationship between them and differentially expressed genes in cassava These AFSM markers were used to generate a genetic linkage map and identify repeatable quantitative trait loci (QTL) and epigenetic quantitative trait loci (QTLepi) based on years of repeated experiments in the greenhouse and field
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