Two recombinant inbred (RI) populations having 194 and 222 lines each, derived, respectively, from a highly heterotic inter-(IJ ) and intrasubspecific (II ) hybrid, were backcrossed to their respective parents. The RI and two backcross populations along with F 1 and its two parents of each hybrid were evaluated for nine important traits, including grain yield and eight other yield-related traits. A total of 76 quantitative trait loci (QTL) for the IJ hybrid and 41 QTL for the II hybrid were detected in the RI population, midparent heterosis of two backcross populations, and two independent sets of data by summation (L 1 1 L 2 ) and by subtraction (L 1 À L 2 ) of two backcross populations (L 1 and L 2 ). The variance explained by each QTL ranged from 2.6 to 58.3%. In the IJ hybrid, 42% (32) of the QTL showed an additive effect, 32% (24) a partial-tocomplete dominant effect, and 26% (20) an overdominant effect. In the II hybrid, 32% (13) of the QTL demonstrated an additive effect, 29% (12) a partial-to-complete dominant effect, and 39% (16) an overdominant effect. There were 195 digenic interactions detected in the IJ hybrid and 328 in the II hybrid. The variance explained by each digenic interaction ranged from 2.0 to 14.9%. These results suggest that the heterosis in these two hybrids is attributable to the orchestrated outcome of partial-to-complete dominance, overdominance, and epistasis. H ETEROSIS, a term to describe the superiority of heterozygous genotypes over their corresponding parental genotypes (Shull 1908), has been under investigation for $100 years, but no consensus exists about the genetic basis underlying this very important phenomenon. Two contending hypotheses, the dominance hypothesis and the overdominance hypothesis, were proposed to explain this phenomenon about one century ago. The dominance hypothesis attributes heterosis to canceling of deleterious or inferior recessive alleles contributed by one parent, by beneficial or superior dominant alleles contributed by the other parent in the heterozygous genotypes at different loci (Davenport 1908;Bruce 1910;Jones 1917). The overdominance hypothesis attributes heterosis to the superior fitness of heterozygous genotypes over homozygous genotypes at a single locus (East 1908;Shull 1908).Molecular markers and their linkage maps have greatly facilitated the identification of individual loci conditioning heterosis and the estimation of gene action of underlying loci. Quantitative trait locus (QTL) mapping studies aiming at understanding the genetic basis of heterosis have been conducted in rice and other crops (Xiao et al. 1995;Li et al. 1997Li et al. , 2001Yu et al. 1997;Luo et al. 2001;Hua et al. 2002Hua et al. , 2003Semel et al. 2006;Frascaroli et al. 2007; Melchinger et al. 2007a,b). Evidence from such studies suggests that heterosis may be attributable to dominance (Xiao et al. 1995;Cockerham and Zeng 1996), overdominance (Stuber et al. 1992;Li et al. 2001;Luo et al. 2001), pseudooverdominance due to tightly linked loci with beneficial ...
BackgroundAmorphophallus is a genus of perennial plants widely distributed in the tropics or subtropics of West Africa and South Asia. Its corms contain a high level of water-soluble glucomannan; therefore, it has long been used as a medicinal herb and food source. Genetic studies of Amorphophallus have been hindered by a lack of genetic markers. A large number of molecular markers are required for genetic diversity study and improving disease resistance in Amorphophallus. Here, we report large scale of transcriptome sequencing of two species: Amorphophallus konjac and Amorphophallus bulbifer using deep sequencing technology, and microsatellite (SSR) markers were identified based on these transcriptome sequences.ResultscDNAs of A. konjac and A. bulbifer were sequenced using Illumina HiSeq™ 2000 sequencing technology. A total of 135,822 non-redundant unigenes were assembled from about 9.66 gigabases, and 19,596 SSRs were identified in 16,027 non-redundant unigenes. Di-nucleotide SSRs were the most abundant motif (61.6%), followed by tri- (30.3%), tetra- (5.6%), penta- (1.5%), and hexa-nucleotides (1%) repeats. The top di- and tri-nucleotide repeat motifs included AG/CT (45.2%) and AGG/CCT (7.1%), respectively. A total of 10,754 primer pairs were designed for marker development. Of these, 320 primers were synthesized and used for validation of amplification and assessment of polymorphisms in 25 individual plants. The total of 275 primer pairs yielded PCR amplification products, of which 205 were polymorphic. The number of alleles ranged from 2 to 14 and the polymorphism information content valued ranged from 0.10 to 0.90. Genetic diversity analysis was done using 177 highly polymorphic SSR markers. A phenogram based on Jaccard’s similarity coefficients was constructed, which showed a distinct cluster of 25 Amorphophallus individuals.ConclusionA total of 10,754 SSR markers have been identified in Amorphophallus using transcriptome sequencing. One hundred and seventy-seven polymorphic markers were successfully validated in 25 individuals. The large number of genetic markers developed in the present study should contribute greatly to research into genetic diversity and germplasm characterization in Amorphophallus.
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