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ARS Home » Southeast Area » Tifton, Georgia » Crop Protection and Management Research » Research » Publications at this Location » Publication #325393
Title: Fine mapping and identification of candidate genes for a QTL affecting Meloidogyne incognita reproduction in Upland cotton

Author
item KUMAR, P - University Of Georgia
item HE, Y - Southwest University
item SINGH, R - University Of Georgia
item Davis, Richard
item GUO, H - University Of Georgia
item PATTERSON, A - University Of Georgia
item PETERSON, D - Mississippi State University
item SHEN, X - Jiangsu Academy Agricultural Sciences
item NICHOLS, R - Cotton, Inc
item CHEE, P - University Of Georgia

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/7/2016
Publication Date: 8/8/2016
Citation: Kumar, P., He, Y., Singh, R., Davis, R.F., Guo, H., Patterson, A.H., Peterson, D.G., Shen, X., Nichols, R.L., Chee, P. 2016. Fine mapping and identification of candidate genes for a QTL affecting Meloidogyne incognita reproduction in Upland cotton. Biomed Central (BMC) Genomics. 17:567. doi:10.1186/s12864-016-2954-1.

Interpretive Summary: The resistant line Auburn 623RNR and a number of elite breeding lines derived from it remain the most important source of root-knot nematode (RKN) resistance because they exhibit the highest level of resistance to RKN known to date in Upland cotton. Prior genetic mapping analysis identified two sections of DNA (QTLs) that impart RKN resistance, qMi-C11 (which affects gall formation) and qMi-C14 (which affects RKN reproduction, but not galling). Herein, we developed a cotton population segregating only for the qMi-C14 locus and evaluated the genetic effects of this QTL on RKN resistance in the absence of the qMi-C11 locus. The locus qMi-C14 accounted for 24.5 % of the total phenotypic variation for egg production. In addition to not being significantly associated with gall formation, this locus had less effect on RKN reproduction than our previous study in which both QTLs were present, which lends further support to the theory that the two QTLs interact in imparting RKN resistance in the Auburn 623RNR source. The locus qMi-C14 was fine-mapped with the addition of 16 newly developed markers, offering additional resources to improve the efficiency of marker-assisted selection for this resistance QTL. By using the reference genomic sequence of G. raimondii, a closely related cotton species, we identified 20 candidate genes in a small section of DNA (2.3 Mb region) that could be responsible for the RKN resistance imparted by qMi-C14.

Technical Abstract: The resistant line Auburn 623RNR and a number of elite breeding lines derived from it remain the most important source of root-knot nematode (RKN) resistance because they exhibit the highest level of resistance to RKN known to date in Upland cotton (Gossypium hirsutum L). Prior genetic mapping analysis has identified two epistatically interacting RKN resistance QTLs, qMi-C11 and qMi-C14, affecting gall formation and RKN reproduction, respectively. Herein, we developed a genetic population segregating only for the qMi-C14 locus and evaluated the genetic effects of this QTL on RKN resistance in the absence of the qMi-C11 locus. The locus qMi-C14 had a LOD score of 12 and accounted for 24.5 % of the total phenotypic variation for egg production. In addition to not being significantly associated with gall formation, this locus had a lower main effect on RKN reproduction than our previous study, which lends further support for the role of epistasis with qMi-C11 in imparting RKN resistance in the Auburn 623RNR source. The locus qMi-C14 was fine-mapped with the addition of 16 newly developed markers, offering additional resources to improve the efficiency of marker-assisted selection for this resistance QTL. By using the reference genomic sequence of G. raimondii, we identified 20 candidate genes encoding for disease resistance protein homologs in the newly defined 2.3 Mb region flanked by two SSR markers.