Molecular Karyotypes of Loquat (Eriobotrya
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Wen et al. Plant Methods (2020) 16:22 https://doi.org/10.1186/s13007-020-00568-7 Plant Methods METHODOLOGY Open Access Molecular karyotypes of loquat (Eriobotrya japonica) aneuploids can be detected by using SSR markers combined with quantitative PCR irrespective of heterozygosity Guo Wen† , Jiangbo Dang† , Zhongyi Xie , Jinying Wang, Pengfei Jiang, Qigao Guo and Guolu Liang* Abstract Background: Aneuploidy, a condition caused by an imbalance between the relative dosages of chromosomes, generally produces a novel phenotype specifc to the molecular karyotype. Few techniques are currently available for detecting the molecular karyotypes of aneuploids in plants. Results: Based on this imbalance in chromosome dosage, a new approach (referred to as ‘SSR-qPCR’) combining sim- ple 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 specifc 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. Conclusion: SSR-qPCR can detect loquat aneuploids and be used to construct the entire molecular karyotypes of aneuploid individuals. Therefore, this method ofers a novel alternative for the detection of chromosome aneuploidies. Keywords: Loquat, Aneuploidy, SSR markers, qPCR, Molecular karyotype Background that certain traits are strongly associated with the dos- Aneuploidy can result in partial genome duplication, ages of specifc chromosome types and that chromo- which involves the imbalance between the relative dos- somal efects can be additive in Arabidopsis thaliana. ages of chromosomes [1]. Aneuploidy is usually lethal Some aneuploids are useful for crop production. Guava, in plants [2–4], and the surviving individuals frequently pear and loquat aneuploids have been studied in rela- exhibit novel phenotypic traits specifc to the molecular tion to rootstock selection for dwarfng [5–9]. Moreover, karyotypes. Each of the 12 Datura trisomies results in a aneuploidy in plants is associated with some unique and diferent phenotype, depending on which type of chro- desirable traits, such as multiple petals, male sterility, tol- mosome has trisomy [2]. Henry et al. [1] demonstrated erance of cold or drought or resistance to disease [10–12]. Terefore, research on aneuploidy is of great signifcance *Correspondence: [email protected] for crop production. Te identifcation of aneuploids and †Guo Wen and Jiangbo Dang contributed equally to this work the construction of their complete molecular karyotypes College of Horticulture and Landscape Architecture; Academy of Agricultural Sciences; Key Laboratory of Horticulture Science are fundamental and crucial for such research. for Southern Mountain Regions of Ministry of Education; State Cultivation Many techniques have been widely used for the Base of Crop Stress Biology for Southern Mountainous Land, Southwest detection of chromosome copy number changes in University, Beibei, Chongqing, China aneuploid individuals. Te unquestionable and unique © The Author(s) 2020. 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The Creative Commons Public Domain Dedication waiver (http://creat iveco mmons .org/publi cdoma in/ zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Wen et al. Plant Methods (2020) 16:22 Page 2 of 16 merit of classic cytogenetics and fuorescence in situ irrespective of heterozygosity. Notably, with the publi- hybridization (FISH) is their abilities to produce com- cation of the genome sequences of major crops, more plete karyotypes and reveal balanced major rearrange- SSR markers have become available. ments; however, these techniques are time consuming Loquat (Eriobotrya japonica (Tunb.) Lindl.) originated and labour intensive [13]. Flow cytometry does not in Southwest China, and among the 20 species belonging accurately detect aneuploidy, but simple sequence to the genus Eriobotrya, only loquat is used for commer- repeat (SSR) and single nucleotide polymorphism cial fruit production [23, 24]. Many triploid lines that can (SNP) markers are advantageous for the reliable iden- be derived from unreduced gametes have been selected tifcation of aneuploidy [14]. Many recently developed from progeny of diploid germplasms [25], and some ane- DNA-based methods are faster, less expensive and uploid plants can be derived from triploids [1, 4]. Tese achieve a higher resolution compared with the previ- aneuploid loquat plants are useful for research on the ously available methods. Quantitative fuorescent pol- efects of chromosome dosage on the genomic expression ymerase chain reaction (QF-PCR) is widely applied in and phenotypes of plants. At present, the whole molecu- humans for the prenatal diagnosis of trisomy of chro- lar karyotype of aneuploid loquat is helpful for genomics- mosomes 21, 18, 13, X, and Y [15, 16]. SNP arrays have based research. been used as high-throughput genotyping tools for In this study, we found, for the frst time, that a com- polyploid wheat, potato, sugarcane, and strawberry bination of SSR markers and qPCR (SSR-qPCR) can be crops [17]. Quantitative real-time polymerase chain used to construct the entire molecular karyotypes of reaction (qPCR) has also been used for detection of the aneuploid individuals of E. japonica. Tis approach does trisomy of chromosomes 21 (Down syndrome) and 11 not require large numbers of SSR markers or multiple [18]. qPCR, due to its specifcity, sensitivity and repli- types of fuorescent markers. In addition, this DNA- cability, is widely used for gene expression analysis and based qPCR method does not require additional refer- is one of the most reliable tools for the detection of ence genes, and SSR markers in 17 LGs can be selected nucleic acid sequence copy numbers [13, 19]. However, as cross-references. Te approach is also not restricted the application of qPCR for the detection of aneuploid to heterozygous genotypes. Moreover, SSR-qPCR allows plant molecular karyotypes has rarely been reported. the construction of molecular karyotypes without whole- Previously, aneuploid and polyploid A. thaliana have genome sequence data, and then validated in the of- been detected by measurement of the relative allelic spring populations of triploid lines, and more than 88% ratios of the heterozygous genotype [3]. Te details of of the ofspring of triploids were found to be aneuploid. polyploidization have been described in Malus, with Tese data will be critical for the development of molecu- particular emphasis on aneuploidy, via detection of the lar tools and strategies for loquat breeding programmes. types of heterozygous genotypes and the corresponding frequencies of occurrence [12]. Both of these methods are limited to heterozygous genotypes; in particular, Methods the detection of the occurrence frequencies of het- Plant material erozygous genotypes using statistical methods requires Twenty-three loquat lines with diferent ploidies were large numbers of codominant SSR markers. Similarly, used as the materials in this study (Table 1): 2 Sichuan high-resolution melting (HRM) and multiplex liga- Province cultivars (‘Dawuxing’ and ‘Longquan No. 1’), 2 tion-dependent probe amplifcation (MLPA) are also Zhejiang Province cultivars (‘Ruantiaobaisha’ and ‘Ning- limited to heterozygous genotypes. SSR markers are haibai’), 1 Fujian Province cultivar (‘Changbai No. 1’) randomly distributed throughout the plant genome and 18 excellent strains selected at Southwest University and are reproducible, codominant, and transferable (A313, A322, B350, B352, B353, B356, B431, B456, B460, [20]. Microsatellite markers have been widely used in B432, ‘Wuheguoyu’, H424, H39, 77-1, K474, ‘Huabai No. genetic and paternal studies [21, 22], but they are rarely 1’, Q24 and ‘Huayuwuhe No. 1’). All of these lines were used in molecular karyotypic studies. Codominant obtained from the polyploid loquat germplasm resource markers can be amplifed from allelic loci simultane- nursery at Southwest University, Chongqing, China. In ously by qPCR. When allelic loci are homozygous, the addition, to produce aneuploid strains, we performed ratios between markers from diferent loci are constant hybridization of Q24 (3x) × ‘Huabai No. 1’ (2x), and we between euploids. If there are appropriate SSR mark- selected some hybrids and elucidated their genetic rela- ers in each linkage group (LG) used for qPCR, accurate tionships