## Genetic region of origin varieties that contributed to apple breeding-Development of a method to automatically track the inheritance of haplotypes of origin varieties-
NOTE READ Very Bottom of Article First on link (or see second post on the forum here. )
could give you a better Idea Of what they are explaining (I plan to re read again )
**COPIED FROM HERE **
The Kyushu Okinawa Agricultural Research Center, NARO
ACTUALLY LOOKING UP (but could not find good link)
Okinawa Prefectural Agricultural Research Center located in Nago
Presenter
Mai Minamikawa (
Specially Appointed Researcher, Department of Production and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo: At that time / Currently, Research Fellow of the Japan Society for the Promotion of Science)
Miyuki Kunihisa (Senior Researcher, National Institute of Agrobiological Sciences, Fruit Tree Tea Industry Research Division)
Koji Noshita (Assistant Professor, Plant Frontier Research Center, Graduate School of Science, Kyushu University)
Shigeki Moriya (Senior Researcher, Apple Research Area,
Fruit Tree Tea Industry Research Division, National Institute of Agrobiological Sciences) Kazuyuki Abe (Variety Development Research Area, Fruit Tree Tea Industry Research Division, National Institute of Agrobiological Sciences)
Takeshi Hayashi ( Director, Basic Research Area,
National Institute of Agrobiological Sciences, Next Generation Crop Development Research Center: At that time) Yuichi Katayori (National Institute of Agrobiological Sciences, Agricultural Biological Advanced Genome Research Center, Advanced Genome Analysis Office: At that time /
Currently Agricultural Research Institute mechanism next generation crop development research Center genome breeding research overall audit)
Toshimi Matsumoto (National research and development corporation NIAS agriculture biological tip genome research Center, Advanced genomics room: At the time /
current NARO biological function using research department animal function use Research Area Contract Researcher)
Chikako Nishitani (Senior Researcher, Variety Development Research Area,
Fruit Tree Tea Industry Research Division, National Institute of Agrobiological Sciences) Shingo Terakami ( Senior Researcher, Fruit Tree Tea Industry Research Division, National Institute of Agrobiological Sciences)
Toshiya Yamamoto (Fruit Tree Tea, National Institute of Agrobiological Sciences) Industrial Research Division Variety Development Research Area Unit Director: At that time)
Hiroka Iwata (Associate Professor, Department of Production and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo)
Announcement points
- We have developed a method to automatically track the inheritance of haplotypes (Note 1) of major origin varieties in domestic apple varieties.
- Genome-wide association study (GWAS) (Note 2) revealed haplotypes of origin varieties that may have been used to grow apples with good pericarp coloring.
- In the evaluation of the genomic selection (GS) (Note 3) prediction model, it is possible to predict the malic acid content of fruits with high accuracy, and it is expected that breeding will be more efficient.
Presentation summary
Since domestic apple varieties are mainly derived from seven varieties of origin, it is thought that there are 14 haplotypes (Fig. 1). If the inheritance of these haplotypes can be traced correctly, it may be possible to more accurately understand the diversity of properties of domestic varieties.
Research groups at the University of Tokyo, NARO, and Kyushu University have developed a method to automatically track the inheritance of these 14 haplotypes. By using this method, we were able to represent the genomic region of 92% of all apple individuals tested in the study with 14 types of haplotype information. Genome-wide association studies (GWAS) using this haplotype information revealed haplotypes of origin varieties that may have been used to grow apples with good pericarp coloring. Furthermore, in the evaluation of the genomic selection (GS) prediction model, the malic acid content of fruits was predicted with high accuracy.
Haplotype information of the cultivar of origin can be combined with the genealogy information of the individual to visualize the inheritance, and the history of apple breeding can be unraveled. The haplotype of the promising origin variety newly discovered this time is expected to be used for the development of new varieties in the future.
Announcement content
Figure 1 14 haplotypes in 7 apple-origin varieties
Figure 2 Propagation in one “Worcester Pearmain” haplotype cultivar group involved in apple peel coloring
Pink represents a cultivar with one “Worcester Pearmain” haplotype (Haplotype 10: Figure 1).
Figure 3 Prediction accuracy of the genomic selection (GS) prediction model for fruit malic acid content
Correct tracking of the haplotype inheritance of apple varieties may lead to an accurate understanding of the diversity of properties of domestic varieties, but it is very difficult to do manually. Therefore, in this study, we developed a method to automatically track the inheritance of the haplotype of the cultivar of origin from the information of the genome-wide marker (Note 4) by using a computer algorithm. We also evaluated the prediction accuracy of fruit properties using a genome-wide association study (GWAS) and a genomic selection (GS) prediction model, and examined the possibility of using haplotype information of the varieties of origin.
We tested 185 domestic apple varieties and strains cultivated and maintained by NARO and 659 individuals cultivated from 16 mating combinations. By combining multiple computer algorithms, we have developed a method to automatically track the inheritance of haplotypes of 14 varieties of origin from information on 11,786 genome-wide markers. By using this method, 92% of the genomic regions of all apples used could be represented by 14 haplotype information. When haplotype inheritance was manually tracked and the data was assumed to be correct, the automatically tracked method showed a high correct answer rate of 90%.
Genome-wide association study (GWAS) was performed using the data of cultivars and breeding individuals represented by 14 types of haplotype information. Showed the strongest association. By visualizing the inheritance of this haplotype in light of the genealogy information of the individual, it was revealed that the frequency of this haplotype increased significantly within the population as the generation progressed (Fig. 2). This haplotype may have been used to grow apples with good pericarp coloring. In the accuracy evaluation of the genomic selection (GS) prediction model, the malic acid content of the fruit could be predicted with high accuracy (the correlation coefficient ( r ) (Note 5) between the measured value and the predicted value is greater than 0.6) ( Figure 3). It was also found that when the automatically tracked haplotype information of the cultivar of origin was used, the prediction was more accurate than when the manually tracked haplotype information and the genome-wide marker information were used. (Fig. 3).
From the above results, it is possible to unravel the history of apple breeding by visualizing the inheritance of haplotype information of the cultivar of origin by comparing it with genealogy information. Haplotypes of promising origin varieties are also expected to be used for future new variety development. In addition, genomic selection (GS) using haplotype information of the varieties of origin may improve the efficiency of apple breeding.
By combining haplotypes of promising origin varieties, it is expected that the development of various new varieties that meet the needs of producers and consumers will proceed. The newly developed method for automatically tracking the inheritance of haplotypes of origin varieties can also be applied to allogeneic crops similar to apples. In the future, in order to further improve the accuracy of the method for automatically tracking the haplotype inheritance of the cultivar of origin, we plan to increase the genome-wide marker information of new materials and to investigate the accuracy and appropriate number of genome-wide markers. is.
This research was supported by JSPS Grant-in-Aid for Scientific Research (JP19J40071) and the project “Development of next-generation production basic technology for agricultural products utilizing genomic information” commissioned by the Ministry of Agriculture, Forestry and Fisheries.