A first genetic linkage map of mulberry (Morus spp.) using RAPD, ISSR, and SSR markers and pseudotestcross mapping strategy

Abstract

To lay the foundation for molecular breeding efforts, the first genetic linkage map of mulberry (2n=2x=28) was constructed with 50 F1 full-sib progeny using randomly amplified polymorphic DNA (RAPD), inter-simple sequence repeat (ISSR), and simple sequence repeat (SSR) markers and two-way pseudotestcross mapping strategy. We selected 100 RAPD, 42 ISSR, and 9 SSR primers that amplified 517 markers, of which 188 (36.36%) showed a test-cross configuration, corresponding to the heterozygous condition in one parent and null in the other. Two separate female and male maps were constructed using 94 each of female-and male-specific testcross markers, containing 12 female linkage groups and 14 male linkage groups. At a minimum logarithm of the odds (LOD) score threshold of 6.0 and at a maximum map distance of 20 cM, the female map covered a 1,196.6-cM distance, with an average distance of 15.75 cM and maximum map distance of 37.9 cM between two loci; the male-specific map covered a 1,351.7-cM distance, with an average distance of 18.78 cM and a maximum map distance between two loci is of 34.7 cM. The markers distributed randomly in all linkage groups without any clustering. All 12 linkage groups in the female-specific map consisted of 4-10 loci ranging in length from 0 to 140.4 cM, and in the malespecific map, the 13 largest linkage groups (except linkage group 12, which contained three loci) consisted of 4-12 loci, ranging in length from 53.9 to 145.9 cM and accounting for 97.22% of the total map distance. When mapping, progeny pass through their juvenile phase and assume their adult characters, mapping morphological markers and identification of quantitative trait loci for adaptive traits will be the primary target. In that sense, our map provides reference information for future molecular breeding work on Morus and its relatives.

A linkage map for flowering dogwood (Cornus florida L.) based on microsatellite markers

“…Unlike inbred species, out-crossing species are highly heterozygous and generally not easy to obtain a pedigree from crosses between inbred lines (Venkateswarlu et al 2006). When attempting to build a genetic linkage map, the mapping population is the main issue for the crossing parents (Maliepaard et al 1997).…”

“…F 1 full-sib progeny (Maliepaard et al 1997;Venkateswarlu et al 2006) and BC 1 population (Lalli et al 2008) were also used as mapping population in the linkage analysis of out-crossing trees. Individual linkage maps produced by these methods may lead to inaccuracy in the estimation of recombination frequencies (Venkateswarlu et al 2006).…”

“…Due to high heterozygousity in out-breeding species, an F 1 population pseudo-testcross strategy has been widely used for linkage analysis (Grattapaglia and SederoV 1994;Arcade et al 2000;Porceddu et al 2002;Hanley et al 2002;Barcaccia et al 2003;La Rosa et al 2003;DoucleV et al 2004;Dirlewanger et al 2004;Graham et al 2004;Beedanagari et al 2005;Kenis and Keulemans 2005;Verde et al 2005;Lanteri et al 2006;Lowe and Walker 2006;Mandl et al 2006). Other mapping populations such as F 1 full-sib progeny (Maliepaard et al 1997;Venkateswarlu et al 2006) and BC 1 mapping populations (Lalli et al 2008) have also been used for linkage map construction. In a pseudo-testcross, a single full-sib population is generated by crossing two parents in which one parent is heterozygous at one locus, and the other parent is homozygous at other loci (Mandl et al 2006).…”

Isolation and characterization of genomic microsatellite markers for small cardamom (Elettaria cardamomum Maton) for utility in genetic diversity analysis

“…Hence SSR coupled with earlier reported markers RAPD, RFLP-PCR, ISSR (Nirmal Babu et al 2012) can be used for differentiating the cultivars and mapping population and for developing linkage maps. Construction of integrated genetic linkage map using RAPD, ISSR and SSR have been reported in different crops (Venkateswarlu et al 2006;Priyamedha et al 2012). This report is an initiative towards molecular profiling of more unexploited accessions of small cardamom that can provide insights into patterns of genetic diversity.…”

SSR-based genetic maps of Miscanthus sinensis and M. sacchariflorus, and their comparison to sorghum

“…An intraspecific cross of Morus spp. (mulberry) generated 61.3% bi-parental markers, facilitating the assembly of a consensus map (Venkateswarlu et al 2006). While we could not integrate the two parental maps using bi-parental markers due to their rarity, homologous chromosomes between MSA and MSI could be indirectly determined by aligning linkage groups to the sorghum genome as a reference.…”