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Title:   Author  item
                                            Saha, Sukumaritem
                                            STELLY, DAVID - Texas A&M Universityitem
                                            RASKA, DWAINE - Texas A&M Universityitem
                                            WU, JIXIANG - South Dakota State Universityitem
                                            Jenkins, Johnieitem
                                            McCarty, Jackitem
                                            MAKAMOV, ABDUSALOM - Uzbekistan Academy Of Sciencesitem
                                            GOTMARE, V - Indian Agricultural Research Instituteitem
                                            ABUDURAKHMONOV, IBROKIM - Uzbekistan Academy Of Sciencesitem
                                            Campbell, Benjamin

                                                         - *Todd*
  Submitted to: Book Chapter
                                    Publication Type: Book / Chapter
                                    Publication Acceptance Date: 9/8/2011
                                    Publication  Date: 1/1/2012
                                    Citation: Saha, S., Stelly, D.M., Raska, D.A., Wu, J., Jenkins, J.N., McCarty, Jr., J.C., Makamov, A., Gotmare, V., Abudurakhmonov, I., Campbell, B.T. 2012. Chromosome substitution lines:  Concept, development and utilization in the genetic improvement of upland cotton. In: Abdurakhmoov, I.Y., editor. Plant Breeding. InTech. p. 107-128.Interpretive Summary: The objective of this paper is to provide a summarized report on the development and utilization of chromosome substitution lines (CS) in genetic analysis and germplasm improvement of Upland cotton. A representative type of the original monosomic, monotelodisomic and reciprocal translocation (NTN), backcrossed to Texas Marker-1 (TM-1), serves as the recurrent parent, respectively, for developing the chromosome substitution lines.  The Cotton Cytogenetic Collection currently includes chromosome-deficient stocks of G. hirsutum, mainly primary monosomics (missing one chromosome) for 15 of the 26 chromosomes, and monotelodisomics (missing most of one chromosome arm) for 31 of the 52 chromosome arms, including at least four chromosomes not represented among the monosomic stocks. We are utilizing most of these chromosome-deficient stocks in the development of CS lines. Each alien species chromosome substitution line development involves four specific stages: (1) development of the respective TM-1-like hypoaneuploid stock, (2) use of the cytogenetic stock as a recurrent seed parent in a recurrent backcrossing program to  create a monosomic or monotelodisomic F1 substitution stock, followed by (3) inbreeding with the TM-1-like hypoaneuploid stock to recover a euploid disomic substitution line, and (4) confirmation of the cytogenetic and genetic constitution of the disomic lines by cytological analysis and chromosome-specific SSR markers. Seventeen CS-B lines (CS lines from G. barbadense) were developed using the above procedure and released for use in Upland cotton improvement. We could not confirm the genetic identity of all of the CS lines based on molecular markers at the release time because very few chromosome specific molecular markers were available at that time in the public domain. Recently in addition to the cytological analysis, we undertook an assignment to confirm the genetic identity of the CS lines using chromosome specific SSR markers. Most marker results were concordant but some were inconclusive or discordant and investigation to discern the underlying basis is in progress. These substitution lines are nearly isogenic to the common parent TM-1 for 25 chromosome pairs as well as to each other for 24 chromosome pairs. We discussed in this report the comparative analysis of such unique genetic materials for the detection of genetic effects of novel alleles by specific alien chromosomes associated with quantitative traits.  We showed that CS lines can be a useful tool for additional resolution in genetic mapping and for the targeted exploitation of exotic germplasm to improve fiber quality and agronomic traits in cotton breeding programs.
                                Technical Abstract: New alleles useful for agronomic and fiber quality must be discovered and bred into Upland cotton germplasm to remain competitive in the world economy of cotton production. Two of the primary challenges to genetic improvement of cotton are:  1) insufficient information about complex agronomic and fiber traits and 2) under-utilization of diverse germplasm. The tetraploid species G. barbadense, G. tomentosum, and G. mustelinum are useful sources of important genes for pest and disease resistance, and for improved agronomic and fiber traits. Conventional methods of interspecific introgression into cotton typically entail inbreeding immediately after hybridization or after a few backcrosses. A complementary approach is to develop alien chromosome substitution (CS) lines from other species in Upland genetic background. The objective of this paper is to provide a report on the development and utilization of chromosome substitution lines (CS) in genetic analysis and germplasm improvement of Upland cotton. We are utilizing most of these chromosome-deficient stocks in the development of euploid CS lines. Seventeen CS-B lines (CS lines from G. barbadense) were developed based on cytological analysis and released for use in Upland cotton improvement. Recently, in addition to the cytological analysis, we initiated work to confirm the genetic identity of the CS lines using chromosome specific SSR markers. Most marker results were concordant but some were inconclusive or discordant and investigation to detect the underlying basis is in progress. These substitution lines are nearly isogenic to the common parent TM-1 of G. hirsutum  for 25 chromosome pairs, as well as to each other, for 24 chromosome pairs. For high-resolution analysis of QTLs, we are using many of the CS-B lines in development of chromosome-specific recombinant inbred lines. We reported on the comparative analysis of such unique genetic materials for the detection of genetic effects of novel alleles by specific alien chromosomes associated with quantitative traits. We showed in this paper that CS line can be a powerful tool for high resolution genetic mapping of QTLs and used for the targeted exploitation of exotic germplasm to improve fiber quality and agronomic traits in cotton breeding programs.


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