Fingerprinting and genetic purity assessment of rice varieties and hybrids through microsatellite markers

Nethra, N.; Pushpa, C.; Rani, Kumuda; Gowda, Rame; Prasad, S. Rajendra

doi:10.15258/sst.2016.44.3.01

Cited by 2 publications

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“…The genetic purity of hybrid seeds is an essential requirement across their production and marketing because seed contamination would lead to yield loss and poor grain quality, resulting in disputes between farmers and seed sellers (Nandakumar et al, 2004). There are many means of hybrid seed contamination in production plots, such as pollen shedders, fertility restoration of two-line fertile lines, mechanical mixing during harvest and the following post-harvest handling procedures (Bora et al, 2016;Nethra et al, 2016). Currently, in China, approximately half of the hybrid rice varieties are two-line hybrid rice varieties, and fertility conversion is the main factor leading to seed contamination of these varieties.…”

Section: Discussionmentioning

confidence: 99%

Genetic Diversity Analysis of Hybrid Rice Parental Lines and Genetic Purity Assessment of Hybrid Seeds of China

Cai¹,

Lu²,

Liu³

et al. 2020

JAS

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Thirty-five pairs of SSR primers were used for genetic diversity analysis and DNA fingerprinting of 31 hybrid rice core parental lines developed in central- and southern-China using one japonica rice line and three inbred rice lines as the check varieties. The average number of alleles (Na) per SSR locus was 4.02, with a range of two to eight, the effective number of alleles (Ne) was 83.16 with a mean of 2.38, ranging from 1.19 to 4.66. The polymorphic information content (PIC) ranged from 0.16 to 0.79, with an average number of 0.52. The results of the cluster analysis indicated that the check varieties viz., one japonica rice and three inbred rice, were clustered into two groups with similarity coefficients of 0.62 and 0.71 respectively indicating their relatedness. Thirty-one hybrid rice parental lines were clustered into 6 groups according to their different types, pedigrees and regions of development with similarity coefficients of approximately 0.76. The highest genetic similarity coefficient (0.94) was observed between Y58S and C815S, and the lowest (0.63) was observed between Quan9311A and Peiai64S. The purity of one hybrid rice cultivar was tested using characteristic marker and the field test, and it was demonstrated that the purities obtained using the two methods were similar. This research will be helpful for rice breeding, new cultivar registration and seed production.

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Section: Discussionmentioning

confidence: 99%

Genetic Diversity Analysis of Hybrid Rice Parental Lines and Genetic Purity Assessment of Hybrid Seeds of China

Cai¹,

Lu²,

Liu³

et al. 2020

JAS

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SNP genotyping of maize (Zea mays) hybrids and parental inbred lines for genetic purity testing using double digest restriction site-associated DNA sequencing

Srii

Nethra

Umarani

et al. 2021

Seed Science and Technology

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Maize (Zea mays) is the third major cereal crop in the Indian subcontinent, but the crop yields per hectare of Indian maize cultivars are less than half of the global average due to the impurity of seed lots supplied to farmers. In this study, we discovered high-quality Single Nucleotide Polymorphic markers (SNPs) in two widely cultivated maize hybrids and their parental inbreds. Paired-end double digest restriction site-associated DNA sequencing was used to discover SNPs and a total of 30,764,454 reads with a read length of 151 bp per sample were generated. Genotyping of SNPs for maize hybrids ‘MAH 14-5’ and ‘Hema’ revealed a total of 47,812 and 15,815 Genetic Purity Analysis markers, respectively, of which 44,388 and 12,391 were unique with 3,424 being common to both hybrids. Identified SNPs were used to develop primers for Kompetitive Allele-Specific PCR genotyping assays to determine the genetic purity of 10 seed lots and the results were found to correlate with Grow-out-Tests. Thus, the SNPs discovered in this study proved reliable to test the genetic purity of commercial seed lots. Advances in plant molecular breeding tools especially ddRADseq for SNP discovery offer new opportunities to genotype existing cultivars and accelerate the production of genetically pure seeds.

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Fingerprinting and genetic purity assessment of rice varieties and hybrids through microsatellite markers

Cited by 2 publications

References 0 publications

Genetic Diversity Analysis of Hybrid Rice Parental Lines and Genetic Purity Assessment of Hybrid Seeds of China

Genetic Diversity Analysis of Hybrid Rice Parental Lines and Genetic Purity Assessment of Hybrid Seeds of China

SNP genotyping of maize (Zea mays) hybrids and parental inbred lines for genetic purity testing using double digest restriction site-associated DNA sequencing

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