Development of genomics-based genotyping platforms and their applications in rice breeding

• Published in: Current opinion in plant biology 2013-05, Vol.16 (2), p.247-254
• Main Authors: Chen, Haodong, He, Hang, Zhou, Fasong, Yu, Huihui, Deng, Xing Wang
• Format: Article
• Language: English
• Subjects: alleles; chromosome mapping; crop models; DNA Shuffling; genetic background; Genetic Variation; Genomics - methods; Genotype; genotyping; Genotyping Techniques; marker-assisted selection; Oryza - genetics; Oryza - growth & development; Oryza sativa; recurrent selection; rice
• ISSN: 1369-5266; 1879-0356
• DOI: 10.1016/j.pbi.2013.04.002

•We summarized the genomics-based genotyping platforms and their application in rice breeding.•Major genomics-based genotyping platforms include array and next generation sequence.•Genomics-based genotyping platforms promote the efficiency of genes/QTLs identification.•Molecular breeding by design on the genome-wide level needs genomics-based genotyping platforms. Breeding by design has been an aspiration of researchers in the plant sciences for a decade. With the rapid development of genomics-based genotyping platforms and available of hundreds of functional genes/alleles in related to important traits, however, it may now be possible to turn this enduring ambition into a practical reality. Rice has a relatively simple genome comparing to other crops, and its genome composition and genetic behavior have been extensively investigated. Recently, rice has been taken as a model crop to perform breeding by design. The essential process of breeding by design is to integrate functional genes/alleles in an ideal genetic background, which requires high throughput genotyping platforms to screen for expected genotypes. With large amount of genome resequencing data and high-throughput genotyping technologies available, quite a number of genomics-based genotyping platforms have been developed. These platforms are widely used in genetic mapping, integration of target traits via marker-assisted backcrossing (MABC), pyramiding, recurrent selection (MARS) or genomic selection (GS). Here, we summarize and discuss recent exciting development of rice genomics-based genotyping platforms and their applications in molecular breeding.