The National Agricultural Food Research Organization (NARO) and Ishikawa Prefectural University have jointly developed a method to rapidly produce DNA markers in polyploid crops such as potato and sweetpotato, which are difficult to select ideal individuals because of innumerable chromosome combinations in breeding. In order to identify genomic regions related to agronomically important characteristics for DNA marker production, genomic sequencing analysis on a large number of individuals was required previously. By extracting two populations differing in their intended properties and analyzing the mixture of the extracts, we succeeded in reducing the duration of DNA-marker production, which used to take more than one year, to a minimum of two months. It is expected that this technology will improve the efficiency of selection work using DNA markers in breeding cultivars of polyploid crops for traits with huge demand at production sites and consumers such as disease resistance or tuber quality, etc.
Overview
Potato and sweetpotato, which are polyploid crops with four and six sets of chromosomes respectively, can produce innumerable combinations of chromosomes in the progeny obtained from crosses. The number of chromosome combinations are enormous when compared with diploid crops with two sets of chromosomes such as rice, making it difficult and very labor-intensive work to obtain individuals close to the intended genotypes. In order to efficiently select individuals, we have developed DNA markers useful to select disease-resistant or palatable properties. We have begun the trials for laborious work such as identifying the diseases or assessing the tuber quality at the seedling stage in an easier method using the DNA markers.
Until now, when the DNA markers are produced in potatoes, genome sequences have been analyzed individually for large number of progenies obtained from crosses, which tended to be a large-scale work. In addition, because of several data analysis processes, it took more than a year to produce the DNA markers useful to select the nature of interest. As a result, we were unable to respond promptly to diverse needs from the production sites or the actual users.
In an effort to reduce the duration of analysis, we focused on the QTL-seq method to analyze the differences in genomic sequences between the two groups of progenies after crossing with different characteristics of interest. However, because QTL-seq method was developed for diploid crops such as rice, it was not applicable to polyploid crops horboring more than two sets of chromosomes. Therefore, we developed a method to search for useful genes for multiple sets of chromosomes and developed a polyploid QTL-seq method useful to produce DNA markers in polyploid crops by changing the analytical parameters so that differences in sequences can be detected according to the numbers of four (potato) and six (sweetpotato) sets of chromosomes. By using this method, DNA markers can be efficiently produced in a minimum of 2 months from the investigation of the trait of the progenies. In the future, by applying the technology to various cultivar improvement situations for further validating its effectiveness, and by significantly accelerating the development of DNA markers, we can expect rapid cultivar breeding to address the needs of production sites or actual consumers.
