title: Allele mining and enhanced genetic recombination for rice breeding.
abstract: Traditional rice varieties harbour a large store of genetic diversity with potential to accelerate rice improvement. For a long time, this diversity maintained in the International Rice Genebank has not been fully used because of a lack of genome information. The publication of the first reference genome of Nipponbare by the International Rice Genome Sequencing Project (IRGSP) marked the beginning of a systematic exploration and use of rice diversity for genetic research and breeding. Since then, the Nipponbare genome has served as the reference for the assembly of many additional genomes. The recently completed 3000 Rice Genomes Project together with the public database (SNP-Seek) provides a new genomic and data resource that enables the identification of useful accessions for breeding. Using disease resistance traits as case studies, we demonstrated the power of allele mining in the 3,000 genomes for extracting accessions from the GeneBank for targeted phenotyping. Although potentially useful landraces can now be identified, their use in breeding is often hindered by unfavourable linkages. Efficient breeding designs are much needed to transfer the useful diversity to breeding. Multi-parent Advanced Generation InterCross (MAGIC) is a breeding design to produce highly recombined populations. The MAGIC approach can be used to generate pre-breeding populations with increased genotypic diversity and reduced linkage drag. Allele mining combined with a multi-parent breeding design can help convert useful diversity into breeding-ready genetic resources.
authors.affiliation: Plant Breeding Genetics and Biotechnology Division and International Rice Research Institute, Los Banos, Philippines. h.leung@irri.org.
authors.forename: Hei
authors.initials: H
authors.lastname: Leung
authors.affiliation: Plant Breeding Genetics and Biotechnology Division and International Rice Research Institute, Los Banos, Philippines.
authors.forename: Chitra
authors.initials: C
authors.lastname: Raghavan
authors.affiliation: Plant Breeding Genetics and Biotechnology Division and International Rice Research Institute, Los Banos, Philippines.
authors.forename: Bo
authors.initials: B
authors.lastname: Zhou
authors.affiliation: Plant Breeding Genetics and Biotechnology Division and International Rice Research Institute, Los Banos, Philippines.
authors.forename: Ricardo
authors.initials: R
authors.lastname: Oliva
authors.affiliation: Plant Breeding Genetics and Biotechnology Division and International Rice Research Institute, Los Banos, Philippines.
authors.forename: Il Ryong
authors.initials: IR
authors.lastname: Choi
authors.affiliation: Plant Breeding Genetics and Biotechnology Division and International Rice Research Institute, Los Banos, Philippines.
authors.forename: Vanica
authors.initials: V
authors.lastname: Lacorte
authors.affiliation: Plant Breeding Genetics and Biotechnology Division and International Rice Research Institute, Los Banos, Philippines.
authors.forename: Mona Liza
authors.initials: ML
authors.lastname: Jubay
authors.affiliation: Plant Breeding Genetics and Biotechnology Division and International Rice Research Institute, Los Banos, Philippines.
authors.forename: Casiana Vera
authors.initials: CV
authors.lastname: Cruz
authors.affiliation: Plant Breeding Genetics and Biotechnology Division and International Rice Research Institute, Los Banos, Philippines.
authors.forename: Glenn
authors.initials: G
authors.lastname: Gregorio
authors.affiliation: Plant Breeding Genetics and Biotechnology Division and International Rice Research Institute, Los Banos, Philippines.
authors.forename: Rakesh Kumar
authors.initials: RK
authors.lastname: Singh
authors.affiliation: T.T. Chang Genetic Resource Center, International Rice Research Institute, Los Banos, Philippines.
authors.forename: Victor Jun
authors.initials: VJ
authors.lastname: Ulat
authors.affiliation: T.T. Chang Genetic Resource Center, International Rice Research Institute, Los Banos, Philippines.
authors.forename: Frances Nikki
authors.initials: FN
authors.lastname: Borja
authors.affiliation: T.T. Chang Genetic Resource Center, International Rice Research Institute, Los Banos, Philippines.
authors.forename: Ramil
authors.initials: R
authors.lastname: Mauleon
authors.affiliation: T.T. Chang Genetic Resource Center, International Rice Research Institute, Los Banos, Philippines.
authors.forename: Nickolai N
authors.initials: NN
authors.lastname: Alexandrov
authors.affiliation: T.T. Chang Genetic Resource Center, International Rice Research Institute, Los Banos, Philippines.
authors.forename: Kenneth L
authors.initials: KL
authors.lastname: McNally
authors.affiliation: T.T. Chang Genetic Resource Center, International Rice Research Institute, Los Banos, Philippines.
authors.forename: Ruaraidh
authors.initials: R
authors.lastname: Sackville Hamilton
keywords: Disease resistance; Genetic diversity; MAGIC; SNP database