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1. chinaXiv:202002.00074 [pdf]

Molecular karyotypes of loquat (Eriobotrya japonica) aneuploids can be detected by using SSR markers combined with quantitative PCR irrespective of heterozygosity

Wen, Guo; Dang, Jiangbo; Xie, Zhongyi; Wang, Jinying; Jiang, Pengfei; Guo, Qigao; Liang, Guolu
Comment:This article has been published online in Plant Methods (https://plantmethods.biomedcentral.com/articles/10.1186/s13007-020-00568-7)
Subjects: Biology >> Botany
Subjects: Agriculture, Forestry,Livestock & Aquatic Products Science >> Horticulture

Background: Aneuploidy, a condition caused by an imbalance between the relative dosages of chromosomes, generally produces a novel phenotype specific to the molecular karyotype. Few techniques are currently available for detecting the molecular karyotypes of aneuploids in plants. Methods: By PCR amplification of 209 pairs of SSR primers, 17 pairs of SSR primers with no polymorphism and stable amplification in 23 different ploidy loquat were screened out. Seventeen SSR markers combined with qPCR for detection of aneuploid loquat H39 (2n=2x+5=39) karyotype variation. To verify the method for detection of aneuploid karyotype variation, 9 hybrid offspring of Q24 × ‘Huabai No. 1’ and 16 open-pollination progeny of the triploid loquat A313 and A322 were obtained, and we detected their chromosome numbers using conventional cytological methods. The SSR-qPCR method was used to detect the molecular karyotypes of aneuploids in the 9 hybrid offspring of Q24 × ‘Huabai No. 1’ and 16 open-pollination progeny of the triploid loquat A313 and A322. Results: Based on this imbalance in chromosome dosage, a new approach (referred to as ‘SSR-qPCR’) combining simple sequence repeat (SSR) markers and quantitative real-time PCR (qPCR) has been developed and utilized to detect some common aneuploids irrespective of heterozygosity. We screened 17 specific SSR markers covering all loquat linkage groups and redesigned 6 pairs of primers for SSR markers that can detect loquat chromosome aneuploidies. The SSR-qPCR detection results obtained for hybrid progeny and open-pollination progeny of triploid loquat showed diagnostic accuracies of 88.9% and 62.5%, respectively, compared with the chromosome preparation results. Limitations: Loquat genome sequences have not been published, available SSR markers are currently limited. Conclusion: SSR-qPCR can detect loquat aneuploids and be used to construct the entire molecular karyotypes of aneuploid individuals. Therefore, this method offers a novel alternative for the detection of chromosome aneuploidies.

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