title: Effects of genome structure variation, homeologous genes and repetitive DNA on polyploid crop research in the age of genomics.
abstract: Compared to diploid species, allopolyploid crop species possess more complex genomes, higher productivity, and greater adaptability to changing environments. Next generation sequencing techniques have produced high-density genetic maps, whole genome sequences, transcriptomes and epigenomes for important polyploid crops. However, several problems interfere with the full application of next generation sequencing techniques to these crops. Firstly, different types of genomic variation affect sequence assembly and QTL mapping. Secondly, duplicated or homoeologous genes can diverge in function and then lead to emergence of many minor QTL, which increases difficulties in fine mapping, cloning and marker assisted selection. Thirdly, repetitive DNA sequences arising in polyploid crop genomes also impact sequence assembly, and are increasingly being shown to produce small RNAs to regulate gene expression and hence phenotypic traits. We propose that these three key features should be considered together when analyzing polyploid crop genomes. It is apparent that dissection of genomic structural variation, elucidation of the function and mechanism of interaction of homoeologous genes, and investigation of the de novo roles of repeat sequences in agronomic traits are necessary for genomics-based crop breeding in polyploids.
authors.affiliation: Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang 330045, China. Electronic address: fudhui@163.com.
authors.forename: Donghui
authors.initials: D
authors.lastname: Fu
authors.affiliation: Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany.
authors.forename: Annaliese S
authors.initials: AS
authors.lastname: Mason
authors.affiliation: Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang 330045, China.
authors.forename: Meili
authors.initials: M
authors.lastname: Xiao
authors.affiliation: Key Laboratory of Poyang Lake Basin Agricultural Resources and Ecology of Jiangxi Province, Jiangxi Agricultural University, Nanchang 330045, China.
authors.forename: Hui
authors.initials: H
authors.lastname: Yan
mesh_terms: D002874:Chromosome Mapping / Q000379:methods; D018556:Crops, Agricultural / Q000145:classification / Q000235:genetics*; D018506:Gene Expression Regulation, Plant; D014644:Genetic Variation; D018745:Genome, Plant / Q000235:genetics*; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D011123:Polyploidy; D040641:Quantitative Trait Loci / Q000235:genetics; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics
keywords: Genomic variations; Homoeologous sequences; Polyploids; Repetitive DNA sequences; Transposons