Identification of genes that were differentially expressed and associated with fiber yield and quality using cDNA-AFLP and a backcross inbred line population

Numerous quantitative trait loci (QTLs) have been identified from segregating hybrid populations between Upland (Gossypium hirsutum) and Pima (G. barbadense) cotton. However, the genetic basis of these QTLs is currently unknown. In the present study, an interspecific backcross inbred line (BIL) population was tested at two locations in 2005 and 2006, and used to identify and isolate polymorphic transcript-derived fragments (TDFs) based on complementary DNA (cDNA)-amplified fragment length polymorphism (AFLP) analysis. The BILs were developed from a cross between Upland SG 747 as the recurrent parent and Pima S-7, followed by two generations of backcrossing and three generations of selfing. Of a total of 675 cDNA-AFLP fragments amplified from 15 primer combinations, 143 loci showed qualitative differences (TDFs) among BILs, and 44 TDF loci were significantly correlated with fiber yield and quality traits. Of the more than half of the TDFs cloned and sequenced, 47.4% had unknown function and many were converted to sequence tagged site (STS) markers. The identification of indels was informative in resolving homologous sequences when comparing cDNA-AFLP libraries from the same primer combination among Upland SG 747, Acala 1517-99, and Pima Phy 76. Differential expression of selected subset of TDFs associated with fiber traits was detected by reverse transcription-polymerase chain reaction (RT-PCR) using ovaries of eight selected BILs at 10 days post anthesis (DPA), and SG 747 and Pima 76 at 0, 4, 8, and 13 days. Quantitative RT-PCR was further used for validation on five TDFs using ovaries of Acala 1517-99 and Pima Phy 76 from the four early boll developmental stages. The present study has identified a number of genes whose expression was associated with fiber yield and quality traits.