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United States Department of Agriculture

Agricultural Research Service

Title: Temporal changes on genetic diversity in a sugarcane breeding population using TRAP markers

item Edme, Serge
item Suman, Andru
item Kimbeng, Collins

Submitted to: Plant Genome Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 10/20/2006
Publication Date: 12/5/2006
Citation: Edme, S.J., Suman, A., Kimbeng, C. 2006. Temporal changes on genetic diversity in a sugarcane breeding population using TRAP markers. Plant Genome Conference Proceedings. P201 PAG XV, 2007

Interpretive Summary:

Technical Abstract: The potential effect of a genetic bottleneck or founder event may explain the reduced level of genetic diversity observed in sugarcane (Saccharum spp.) breeding populations, which were founded on a very small group of interspecific clones. Understanding the impact of plant breeding in reducing this diversity is relevant in order to achieve substantial genetic gains. The purpose of this study was to assess the genetic structure of the Canal Point sugarcane breeding populations from the temporal changes in allelic diversity, polymorphism information content (PIC), observed (Ho) and expected (He) heterozygosity, and changes in the variance of linkage disequilibrium. The patterns of genetic diversity were analyzed among 61 sugarcane genotypes including wild progenitors, early hybrids founders, and cultivars released from 1955 to 2000. These genotypes were divided into seven uneven populations which were characterized phenotypically and with molecular markers using sucrose-related target region amplification polymorphism (TRAP) primers. Genetic distance was substantial among the genotypes (ranging from 0.04 to 0.30 with an average of 0.22), but low among the populations (ranging from 0.0275 to 0.0845). The most similar populations were POP2 (early hybrids) with POP3 (F-cultivars), and POP5 (CP70-CP80 cultivars) with POP7 (CP92-CP99 cultivars). POP1 (wild relatives), POP4 (CP50-CP70), and POP6 (CP84-CP89) formed each a separate group. AMOVA revealed genetic differentiation among the seven populations with, however, 96% of the total variation being the within-population component. Percent polymorphism increased from 26.4% in the first decade to 56.15% in the last decade with 58.3% overall. Under a random model, the differences in allelic counts were significant between POP1 and POP2 to POP7. All the TRAP markers were found to be selectively neutral based on the Ewens-Watterson test of neutrality. Moreover, extracting the variance components of linkage disequilibrium based on Ohta’s method revealed that genetic drift with little recombination (D’IS2 > D’ST2 and DST2 > DIS2), not epistatic selection, was responsible for the majority of the associations among the markers. Bayesian inference analysis of the genetic structure indicated that there are genetic differences among the populations with evidence of inbreeding (FIS=0.49±0.29, 'B = FST=0.05±0.005, HS=0.22±0.002, HT=0.23±0.002, GST-B=0.04±0.004).

Last Modified: 06/26/2017
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