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Figure). Similar sets of differentially regulated biological pathways were identified for L1U vs. DSU and B713U vs. DSU (Fig. 4). Fig. 4. Gene ontology categories of differentially expressed transcripts between genotypes without R. reniformis infestation. The percentage of differentially expressed transcripts differing between genotypes in each biological pathway category is shown. A transcript was considered to be differentially expressed if the FDR corrected P-value is smaller than 0.01 and the fold change value is more than 2. Association of differentially expressed transcripts to R. reniformis resistance QTLs The sequences of six SSR markers (BNL3279, BNL4011, BNL1721, BNL569, BNL1551, and GH132), genetically linked to RN resistance QTLs [25,68], were retrieved from the cotton EST database [69]. Five of these SSR marker sequences (all except BNL1721 that only mapped to G. raimondii genome) mapped to both the G. arboreum [21] and the G. raimondii [19] genomes (Table 9). Table 9. Mapping positions of RN resistance QTLs-associated SSR markers SSR BNL3279 BNL4011 BNL569 BNL1551 GH132 BNL3279 BNL4011 BNL1721 BNL569 BNL1551 GH132 Sequence length (bp) 619 337 228 210 739 619 337 241 228 210 739 Chromosome A2 Chr10 A2 Chr4 A2 Chr13 A2 Chr4 A2 Chr10 D5 Chr7 D5 Chr7 D5 Chr13 D5 Chr13 D5 Chr7 D5 Chr7 Start 74030524 133838455 57120961 110408238 14211757 56142481 54550456 30666694 47353483 49018320 53372611 End 74029915 133838116 57121190 110408414 14211051 56143089 54551582 30666468 47353704 49018506 53372033
