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Review
. 2022 Nov 1;12(11):1752.
doi: 10.3390/life12111752.

Utilization of Genotyping-by-Sequencing (GBS) for Rice Pre-Breeding and Improvement: A Review

Vincent Pamugas Reyes  1 , Justine Kipruto Kitony  1 , Shunsaku Nishiuchi  1 , Daigo Makihara  2 , Kazuyuki Doi  1
Affiliations
Review

Utilization of Genotyping-by-Sequencing (GBS) for Rice Pre-Breeding and Improvement: A Review

Vincent Pamugas Reyes et al. Life (Basel). .

Abstract

Molecular markers play a crucial role in the improvement of rice. To benefit from these markers, genotyping is carried out to identify the differences at a specific position in the genome of individuals. The advances in sequencing technologies have led to the development of different genotyping techniques such as genotyping-by-sequencing. Unlike PCR-fragment-based genotyping, genotyping-by-sequencing has enabled the parallel sequencing and genotyping of hundreds of samples in a single run, making it more cost-effective. Currently, GBS is being used in several pre-breeding programs of rice to identify beneficial genes and QTL from different rice genetic resources. In this review, we present the current advances in the utilization of genotyping-by-sequencing for the development of rice pre-breeding materials and the improvement of existing rice cultivars. The challenges and perspectives of using this approach are also highlighted.

Keywords: DNA markers; NGS; genomic selection; molecular breeding.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Conventional scheme for gene discovery and breeding. Materials in the hatched blue box are suitable to apply GBS.
Figure 2
Figure 2
Schematic diagram of a simplified implementation of genomic selection in rice.
Figure 3
Figure 3
General drawbacks of GBS. (A) missing reads resulting in missing genotypes. (B) sequencing errors resulting in incorrect genotypes. (C) undercalled heterozygosity, SNP4 of progeny 2 is likely to be “H” (heterozygous) but called as “A” (same as parent A). Hyphens (“-”) indicate monomorphic sites. Letters highlighted in gray represent the type of drawback.
Figure 4
Figure 4
Visual representation of imputation and error correction in GBS data. Black = missing data, Blue = parent 1, Orange = parent 2, Green = heterozygous allele.
See this image and copyright information in PMC

References

    1. International Rice Genome Sequencing Project. Sasaki T. The map-based sequence of the rice genome. Nature. 2005;436:793–800. doi: 10.1038/nature03895. - DOI - PubMed
    1. Ashikari M., Matsuoka M. Identification, isolation and pyramiding of quantitative trait loci for rice breeding. Trends Plant Sci. 2006;11:344–350. doi: 10.1016/j.tplants.2006.05.008. - DOI - PubMed
    1. Fan C., Xing Y., Mao H., Lu T., Han B., Xu C., Li X., Zhang Q. GS3, a Major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theor. Appl. Genet. 2006;112:1164–1171. doi: 10.1007/s00122-006-0218-1. - DOI - PubMed
    1. Doi K., Izawa T., Fuse T., Yamanouchi U., Kubo T., Shimatani Z., Yano M., Yoshimura A. Ehd1, a B-type response regulator in rice, confers short-day promotion of flowering and controls FT-like gene expression independently of Hd1. Genes Dev. 2004;18:926–936. doi: 10.1101/gad.1189604. - DOI - PMC - PubMed
    1. Brar D.S., Dalmacio R., Elloran R., Aggarwal R., Angeles R., Khush G.S. Gene transfer and molecular characterization of introgression from wild Oryza species into rice. In: Khush G.S., Hettel G., Rola T., editors. Rice Genetics III (In 2 Parts), Proceedings of the Third International Rice Genetics Symposium, Manila, Philippines, 16–20 October 1995. World Scientific; Singapore: 2008. pp. 477–486.

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