title: Bulked sample analysis in genetics, genomics and crop improvement.
abstract: Biological assay has been based on analysis of all individuals collected from sample populations. Bulked sample analysis (BSA), which works with selected and pooled individuals, has been extensively used in gene mapping through bulked segregant analysis with biparental populations, mapping by sequencing with major gene mutants and pooled genomewide association study using extreme variants. Compared to conventional entire population analysis, BSA significantly reduces the scale and cost by simplifying the procedure. The bulks can be built by selection of extremes or representative samples from any populations and all types of segregants and variants that represent wide ranges of phenotypic variation for the target trait. Methods and procedures for sampling, bulking and multiplexing are described. The samples can be analysed using individual markers, microarrays and high-throughput sequencing at all levels of DNA, RNA and protein. The power of BSA is affected by population size, selection of extreme individuals, sequencing strategies, genetic architecture of the trait and marker density. BSA will facilitate plant breeding through development of diagnostic and constitutive markers, agronomic genomics, marker-assisted selection and selective phenotyping. Applications of BSA in genetics, genomics and crop improvement are discussed with their future perspectives.
authors.affiliation: Institute of Crop Science, National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Cheng
authors.initials: C
authors.lastname: Zou
authors.affiliation: Institute of Crop Science, National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Pingxi
authors.initials: P
authors.lastname: Wang
authors.affiliation: Institute of Crop Science, National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China. y.xu@cgiar.org.|International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico. y.xu@cgiar.org.
authors.forename: Yunbi
authors.initials: Y
authors.lastname: Xu
mesh_terms: D001947:Breeding; D018556:Crops, Agricultural / Q000235:genetics* / Q000502:physiology; D005823:Genetics; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D017422:Sequence Analysis, DNA
keywords: DNA-seq; RNA-seq; breeding; bulked sample analysis; bulked segregant analysis; chips; microarrays; protein-seq