Validation of the generality of molecular markers for seedless fruit in grape

Abstract: 【Objective】The natural population of grape (Vitis vinifera L.) was used to evaluate the universality of 9 molecular markers for seedless fruit in order to provide technical support for the breeding of new seedless grape varieties.【Methods】DNA was extracted from healthy and young samples of a natural population consisting of 88 seedless germplasmes and 120 nucleated germplasmes. PCR amplification was performed using 9 reported molecular markers for seedless fruit of grape. Then, the PCR products were detected by 1.5% agarose gel electrophoresis and capillary electrophoresis, and the specific bands were analyzed. The accuracy rate and seedless detection rate were calculated respectively to verify the versatility of 9 molecular markers for seedless fruit of grape.【Results】Among 208 grape germplasmes, 16 germplasmes were detected by SCAR marker GSLP1- 569, including 14 seedless germplasmes and 2 seeded germplasmes. The 14 seedless varieties were Summer Black, Changwuhebai Etc. among others. And, among them, 12 germplasmes were Thompson Seedless and its derivatives. The identification accuracy and nuclear-free detection rate were 57.12% and 90.51%, respectively. Additionally, the 1080 bp specific band was amplified by SCC8-1080 in 53 seedless germplasmes and 19 seeded germplasmes, and the statistical identification accuracy and seedless detection rate were 72.20% and 79.18%, respectively. Moreover, the 2000 bp specific band was amplified by SCF27-2000 in 87seedless germplasmes and 55 seeded germplasmes. The statistical identification accuracy and seedless detection rate were 75.38% and 67.82%, respectively. Furthermore, a total of 6 isotopic point and 8 genotypes were detected by the SSR marker p1-VvAGL11. The chi-square test showed that the allele 250 bp was significantly correlated with the nuclear-free phenotype and 257 bp was significantly correlated with nucleated phenotype. The genotype 250/250 was significantly correlated with the nuclear-free phenotype, and the genotype 257/257 was significantly correlated with the nuclear phenotype. The statistical identification accuracy and nuclear-free detection rate of the marker were 88.47% and 87.74%, respectively. A total of 3 isotopic point and 5 genotypes were detected by the marker p2-VvAGL11. The chi-square test showed that the allele 171 bp was significantly correlated with the nuclear- free phenotype. The 158 bp was significantly correlated with the nuclear phenotype. The genotype 158/171 was significantly correlated with the seedless phenotype, and the genotype 158/158 was significantly correlated with the nuclear phenotype. The accuracy of marker identification and seedless detection rate were 67.43% and 77.22%, respectively. A total of 14 isotopic point and 30 genotypes were detected by the marker p3-VvAGL11. The chi-square test showed that the allele 195 bp was significantly correlated with the nuclear- free phenotype and 185 bp was significantly correlated with the nucleated phenotype. The genotype 185/195 was significantly associated with the nuclear- free phenotype. The genotype 185/185 was significantly correlated with the nuclear phenotype, and the accuracy and nuclear- free detection rate of the marker were 71.94% and 90.72%, respectively. A total of 24 isotopic point and 75 genotypes were detected by the marker 5U_VviAGL11. The chi- square test indicated that the allele 315 bp was significantly correlated with the nuclear-free phenotype and 305 bp was significantly associated with nucleated phenotype. The genotype 307/315 was significantly correlated with the nuclear-free phenotype. The accuracy and nuclear-free detection rate of the marker were 68.47% and 90.80%, respectively. A total of 8 isotopic point were detected in the marker VMC7F2, and the allele 197 bp was significantly correlated with the seedless phenotype by chi-square test. 199 bp was significantly correlated with one phenotype. The genotype 197/199 was significantly associated with the nuclear-free phenotype. The genotype 199/199 was significantly correlated with the nuclear phenotype, and the accuracy and non-nuclear detection rate of the marker were 67.99% and 79.10%, respectively. A total of 9 isotopic point and 21 genotypes were detected by the marker VVSD10. The chi-square test showed that the allele 105 bp was significantly correlated with the nuclear- free phenotype, and the genotype 105/105 was significantly correlated with the nuclear- free phenotype. The identification accuracy and nuclear- free detection rate of the marker were 61.60% and 63.03%, respectively.【Conclusion】Among the SCAR type markers, SCF27-2000 had the highest accuracy and true positive rate, and the performance was the best. And, GSLP1-569 was more suitable for the hybrid offspring of Thompson seedless series. Among the SSR markers, p1-VvAGL11 had good accuracy and seedless detection rate, and the false negative and false positive were low, showing the best performance, while p3-VvAGL11 and 5U_VviAGL11 had higher seedless detection rate, and 5U_VviAGL11 contained more genetic information.