Effective identification of varieties by nucleotide polymorphisms and its application for essentially derived variety identification in rice

Abstract

Background Plant variety identification is the one most important of agricultural systems. Development of DNA marker profiles of released varieties to compare with candidate variety or future variety is required. However, strictly speaking, scientists did not use most existing variety identification techniques for “identification” but for “distinction of a limited number of cultivars,” of which generalization ability always not be well estimated. Because many varieties have similar genetic backgrounds, even some essentially derived varieties (EDVs) are involved, which brings difficulties for identification and breeding progress. A fast, accurate variety identification method, which also has good performance on EDV determination, needs to be developed. Results In this study, with the strategy of “Divide and Conquer,” a variety identification method Conditional Random Selection (CRS) method based on SNP of the whole genome of 3024 rice varieties was developed and be applied in essentially derived variety (EDV) identification of rice. CRS is a fast, efficient, and automated variety identification method. Meanwhile, in practical, with the optimal threshold of identity score searched in this study, the set of SNP (including 390 SNPs) showed optimal performance on EDV and non-EDV identification in two independent testing datasets. Conclusion This approach first selected a minimal set of SNPs to discriminate non-EDVs in the 3000 Rice Genome Project, then united several simplified SNP sets to improve its generalization ability for EDV and non-EDV identification in testing datasets. The results suggested that the CRS method outperformed traditional feature selection methods. Furthermore, it provides a new way to screen out core SNP loci from the whole genome for DNA fingerprinting of crop varieties and be useful for crop breeding.

Whole Genome Sequencing and Morphological Trait-Based Evaluation of UPOV Option 2 for DUS Testing in Rice

“…With the development of sequencing and the reduction of sequencing costs, SNPs have become important molecular markers for diversity analysis. SNPs can be used to perform genome-wide association studies (Huang et al, 2012;Wang et al, 2020) and the rapid identification of highthroughput varieties (Yuan et al, 2022). In this study, based on the whole-genome resequencing of 122 rice germplasms, the screened 37,929 SNP loci were used to analyze the correlation between the molecular and phenotypic distances of rice varieties.…”

Impact of breeder seed multiplication and certified quality seed distribution on rice production in India

“…In addition to seed production within the country, aided with the government support, seeds of inbred and F 1 hybrid cultivars can be multiplied abroad to enable a higher participation in international seed trade. Trait-specific SNP and fingerprint markers are used to validate phenotypic data of rice landraces and cultivars for fragrance, pericarp color, amylose content, starch pasting properties, gelatinization temperature, resistance to disease, plant pubescence, and plant height (McClung et al 2020;Yuan et al 2022). It is vital to select variety-specific SSR markers and sequence DNA of varieties considered for export to authenticate the varietal distinctiveness.…”

Construction of a SNP fingerprinting of exotic pine germplasm resources in China based on 51K liquid- phased probes

“…The seedling systems have been established in nearly 10 provinces, which have selected and bred nearly 100 varieties of afforestation. However, it is tough to differentiate these pine varieties even species only relying on traditional morphological identification as result of their similar nutritional organs, and their hybrid pine phenotypes combined the characteristics of both parents [6]. The growth cycle of forest trees is long, and the efficiency of breeding will be greatly reduced if the breeding is carried out after the seedlings are mature [7].…”