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Development and use of chromosome segment substitution lines as a genetic resource for crop improvement

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Abstract

Key message

CSSLs are a complete library of introgression lines with chromosomal segments of usually a distant genotype in an adapted background and are valuable genetic resources for basic and applied research on improvement of complex traits.

Abstract

Chromosome segment substitution lines (CSSLs) are genetic stocks representing the complete genome of any genotype in the background of a cultivar as overlapping segments. Ideally, each CSSL has a single chromosome segment from the donor with a maximum recurrent parent genome recovered in the background. CSSL development program requires population-wide backcross breeding and genome-wide marker-assisted selection followed by selfing. Each line in a CSSL library has a specific marker-defined large donor segment. CSSLs are evaluated for any target phenotype to identify lines significantly different from the parental line. These CSSLs are then used to map quantitative trait loci (QTLs) or causal genes. CSSLs are valuable prebreeding tools for broadening the genetic base of existing cultivars and harnessing the genetic diversity from the wild- and distant-related species. These are resources for genetic map construction, mapping QTLs, genes or gene interactions and their functional analysis for crop improvement. In the last two decades, the utility of CSSLs in identification of novel genomic regions and QTL hot spots influencing a wide range of traits has been well demonstrated in food and commercial crops. This review presents an overview of how CSSLs are developed, their status in major crops and their use in genomic studies and gene discovery.

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Abbreviations

CASLs:

Chromosome arm substitution lines

CILs:

Candidate introgression lines

CSILs:

Chromosome segment introgression lines

NGNL:

Next-generation NIL (near isogenic line) library

RCSLs:

Recombinant chromosome substitution lines

SSCTI:

Small-segment chromosome translocations and introgression

SSSL:

Single-segment substitution lines

STAIRS:

Stepped aligned inbred recombinant strains

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Acknowledgements

Authors acknowledge ICAR National Professor Project (F. No. Edn/27/4/NP/2012-HRD) Indian Council for Agricultural Research, Government of India, for financial support. Authors are grateful to Dr. D.S. Brar for critically reviewing an earlier version of the manuscript and constant encouragement. We thank Director, ICAR-IIRR, for support.

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  1. ICAR- National Professor Project, ICAR- Indian Institute of Rice Research, Hyderabad, India

    Divya Balakrishnan, Malathi Surapaneni, Sukumar Mesapogu & Sarla Neelamraju

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  1. Divya Balakrishnan
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  2. Malathi Surapaneni
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  3. Sukumar Mesapogu
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  4. Sarla Neelamraju
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Correspondence to Sarla Neelamraju.

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Communicated by Rajeev K. Varshney.

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Balakrishnan, D., Surapaneni, M., Mesapogu, S. et al. Development and use of chromosome segment substitution lines as a genetic resource for crop improvement. Theor Appl Genet 132, 1–25 (2019). https://doi.org/10.1007/s00122-018-3219-y

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