Abstract
Cassava is the third largest food crop of the world and has strong ability of drought tolerance. In order to evaluate the molecular diversity and to discover novel alleles for drought tolerance in cassava germplasms, we examined a total of 107 abiotic stress related expressed sequence tags—simple sequence repeat (EST-SSR) markers in 134 cassava genotypes coming from planting regions worldwide and performed drought related marker-traits association mapping. As results, we successfully amplified 98 of 107 markers in 97 polymorphic loci and 279 alleles, with 2.87 alleles per locus, gene diversity of 0.48 and polymorphic information content (PIC) of 0.41 on average. The genetic coefficient between every two lines was 0.37 on average, ranging from 0.21 to 0.82. According to our population structure analysis, these samples could be divided into three sub-populations showing obvious gene flow between them. We also performed water stress experiments using 100-day old cassava plants in two years and calculated the drought tolerance coefficients (DTCs) and used them as phenotypes for marker-trait association mapping. We found that 53 markers were significantly associated with these drought-related traits, with a contribution rate for trait variation of 8.60% on average, ranging between 2.66 and 28.09%. Twenty-four of these 53 associated genes showed differential transcription or protein levels which were confirmed by qRT-PCR under drought stress when compared to the control conditions in cassava. Twelve of twenty-four genes were the same differential expression patterns in omics data and results of qRT-PCR. Out of 33 marker-traits combinations on 24 loci, 34 were positive and 53 negative alleles according to their phenotypic effects and we also obtained the typical materials which carried these elite alleles. We also found 23 positive average allele effects while 10 loci were negative according to their allele effects (AAEs). Our results on molecular diversity, locus association and differential expression under drought can prove beneficial to select excellent materials through marker assisted selection and for functional genes research in the future.
Highlights
Cassava, an important food and starch crop, has excellent adaptability to multiple environments
To evaluate the molecular diversity and genetic structure of cassava germplasm resources, we used 107 expressed sequence tags—simple sequence repeat (EST-SSR) markers, 98 of which were located in cassava chromosomes (S1 Fig.) while others were mapped in scaffolds of cassava genome version 6.1
The results of association mapping were supported by reverse genetics evidences as well as previous study, allowing selecting elite alleles of the associated loci
Summary
An important food and starch crop, has excellent adaptability to multiple environments. Seasonal drought every year reduces its yield in major planting regions [1, 2]. One approach to solve this problem is to develop new cultivars which are drought-tolerant and have high yield. Analysis of the genetic diversity of germplasms is a valuable tool for cassava breeding, especially when aiming for drought tolerance [2]. High genetic diversity in germplasm improves the probability to select excellent new germplasms. Genetic diversity is used as a reference to select materials with outstanding characteristics, such as high yield and drought tolerance, and parent materials with excellent breeding potential and multiple elite alleles of interest
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