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. 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 (Quantitative trait loci), genes or gene interactions and their functional analysis for crop improvement.1 CSSLs were first reported as introgression lines in tomato followed by contig lines in rice. The purpose of developing CSSLs is to have a workable set of lines with large segments substituted with homologous donor segments such that these substitutions one by one in a background line make a difference in phenotype for agronomically useful traits.

CSSLs can have tremendous novel variability when distant cultivars or wild species are involved in their development. Novel phenotypic variations observed in CSSLs are mainly due to introduction of new genomic segments, its interaction with background genome and reduced co-segregation of multiple genes. CSSL development strategies mainly involve two steps, first backcross breeding between recurrent and donor parent, second genotyping the backcross progenies for tracking the donor chromosome segments in recurrent background. These two steps are conducted simultaneously, and finally a set of lines each with a specific target chromosome segment is selfed to create a complete CSSL library for further evaluation.

Two pairs of tightly linked QTLs for SER (stigma exsertion rate) on chromosomes 2 (qSER-2a and qSER-2b) and 3 (qSER-3a and qSER-3b) in rice were dissected by substitution mapping using CSSLs.3 The genetic mechanism underlying six palatability properties of cooked rice and three physico-chemical traits was dissected in 66 BC3F2 CSSLs, using a complete linkage map in three successive years4. The CSSL population, constructed by the hybridization of the two strains, contained only one or several import fragments, which was helpful to accurately find important fragments or genes affecting the somatic embryogenesis of soybean. This population was also very important for the study of soybean somatic embryogenesis ability2. It is expected that the development and availability of a genomic resource such as CSSLs in crops will improve the understanding of introgression and adaptive variation and contribute to improvement of major crops to meet global demands to cope with climate change.

References:

1. BALAKRISHNAN, D., SURAPANENI, M., MESAPOGU, S. AND NEELAMRAJU, S., 2019, Development and use of chromosome segment substitution lines as a genetic resource for crop improvement. Theor. Appl. Genet. 132:1-25.

2. LI, S.N., CHENG, P., BAI, Y.Q., SHI, Y., YU, J.Y., LI, R.C., ZHOU, R.N., ZHANG, Z.G., WU, X.X. AND CHEN, Q.S., 2019, Analysis of soybean somatic embryogenesis using chromosome segment substitution lines and transcriptome sequencing. Genes. 10(11):943.

3. TAN, Q., WANG, C., LUAN, X., ZHENG, L., NI, Y., YANG, W., YANG, Z., ZHU, H., ZENG, R., LIU, G. AND WANG, S., 2021, Dissection of closely linked QTLs controlling stigma exsertion rate in rice by substitution mapping. Theor. Appl. Genet. 134:1253-1262.

4. WAN, X.Y., WAN, J.M., SU, C.C., WANG, C.M., SHEN, W.B., LI, J.M., WANG, H.L., JIANG, L., LIU, S.J., CHEN, L.M. AND YASUI, H., 2004, QTL detection for eating quality of cooked rice in a population of chromosome segment substitution lines. Theor. Appl. Genet. 110:71-79.