Narrative
FA5/CU17NBL is a line derived in the CU17NBL acylsugar benchmark breeding line by transferring the FA5 introgression from FA5/CU071026 into CU17NBL. The FA5 QTL was found by looking for differences in fatty acids in acylsugars, but the major impact of FA5 QTL is that it strongly reduces the level of acylsugar. As such, FA5/CU071026 and FA5/CU17NBL are ideal controls for the sister acylsugar lines in CU071026 and CU17NBL backgrounds, respectively. They have all of the introgressions of CU071026 or CU17NBL, respectively, yet produce very little acylsugar. This helps distinguish effect of acylsugar presence vs effect of introgression presence (which include many other genes than those underlying the acylsugar QTL.
The creation of the major Cornell acylsugar lines including CU071026 and CU17NBL is reviewed in the publication Mutschler (2021).
CU17NBL has 5 S. pennellii introgressions which combined are ca. 11% of the CU17NBL genome. The locations and sizes of these locations using the 2.5 genome build are:
• Chromosome 2: the Chr2 introgression, from 53,792,960 - 55,238,304 bp: Therefore, it is 1,445,344 bp in length.
• Chromosome 3: the Chr3 introgression, from 2,143,744 - 64,451,474 bp: Therefore, it is 62,307,730 bp length.
• Chromosome 7: the Chr7 introgression, from 65,554,074 – 65,801,666 bp: Therefore, it is 247,592 bp in length.
• Chromosome 8: the Chr8 introgression, from 60,843,834 – 63,384,503 bp: Therefore, it is 1,445,344 bp in length
• Chromosome 10: the Chr10U introgression, from 0 - 1,916,909 bp: Therefore, it is 2,540,669 bp in length.
The FA5QTL containing introgression was transferred into the prior benchmark line, CU071026, as described in Smeda, 2016. The additional introgression of FA5/CU17NBL is:
• Chromosome 5: the Chr5 introgression, from 61,869,629 bp to 62,738,996 bp on Chromosome 5. Therefore, it is 869,367 bp in length
The source of the FA5QTL create FA5/CU17NBL was the analogous line in CU071026 line, FA5/CU071026. The FA5/CU17NBL line is very similar in acylsugar level and acylsugar types to that of FA5/CU071026. A publication regarding creation and complete characterizations of QTL6/CU17NBL and QTL6/Sw-5/CU17NBL, and other variant lines in CU17NBL is in preparation. Since FA5/CU17NBL contains all of the CH17NBL introgressions, but produces very little acylsugar, due to the presence of FA5 QTL, FA5/CU17NBL would be negative control for CU17NBL and the other CU17NBL derived lines.