Bulked sample analysis in genetics, genomics and crop improvement

Abstract

SummaryBiological 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.

Development of a multiple-hybrid population for genome-wide association studies: theoretical consideration and genetic mapping of flowering traits in maize

“…The populations derived from two parental lines are most widely used in genetics, genomics and breeding, with the following advantages and disadvantages:F 2 : containing sufficient genetic information, but failing to distinguish the genotypes just by phenotyping owing to the presence of heterozygotes, and thus the phenotyping is usually measured with its derived F 2:3 families, progenies produced by bulked pollination of F 2 individuals, and the F 2 genotypes maintained by multiple tillers and ratoning procedures1920.BC 1 : including two types of genotypes which could be distinguished theoretically just by phenotyping if the target gene is dominant, but difficult to maintain the materials for long time, although the genotypes may be maintained by following the procedures for F 2 individuals as discussed above.RIL (recombinant inbred line): consisting of genetically stable genotypes, which can be maintained permanently without change of the population constitution, and suitable for distinguishing dominant and co-dominant statuses, but difficult to be bred for some species, especially for cross-pollinated plants2122.DH (doubled haploid): including homogeneous and breeding-true genotypes and reflecting the gene segregation and recombination rate of F 1 gametes, with different protocols available for the development of DH lines including microspore culture, chromosome elimination, and haploid inducers, depending on crop species1920.…”

“…F 2 : containing sufficient genetic information, but failing to distinguish the genotypes just by phenotyping owing to the presence of heterozygotes, and thus the phenotyping is usually measured with its derived F 2:3 families, progenies produced by bulked pollination of F 2 individuals, and the F 2 genotypes maintained by multiple tillers and ratoning procedures1920.…”

“…DH (doubled haploid): including homogeneous and breeding-true genotypes and reflecting the gene segregation and recombination rate of F 1 gametes, with different protocols available for the development of DH lines including microspore culture, chromosome elimination, and haploid inducers, depending on crop species1920.…”

“…An immortalized F 2 population can be developed through crosses among RIL or DH populations, which can be used permanently for QTL analysis2023.…”

“…There are many types of populations that have been used in genetics, genomics and crop improvement1920. These populations have been used individually, and in very few cases, in combination.…”