Cotton fiber properties are essential predictors of yarn performance. The suite of fiber quality traits that collectively affect the utility of the fiber for the textile industry include the length, the strength, the fineness and the color. These properties have been shown to be moderately to highly heritable. In an attempt to overcome the limitations of conventional breeding we undertook a marker‐assisted selection program aimed at introgressing fiber quality QTLs from Gossypium barbadense L. into G. hirsutum L. We describe the QTL analysis of 11 fiber properties measured on three phenotypic data sets. The three populations studied were the 1st (BC1) and 2nd (BC2 and BC2S1) backcross generations derived from the cross between ‘Guazuncho 2’, G. hirsutum, and ‘VH8’, G. barbadense Collectively we detected 80 QTLs, of which 50 surpassed the permutation‐based LOD thresholds (3.2–5.7). The most economically important traits, length (two correlated properties), strength, fineness (four properties), and color (two properties) were influenced by 15, 12, 21, and 16 QTLs, respectively, that could be detected in one or more populations. As expected, for the majority of QTLs, the favorable alleles came from the G. barbadense parent. Altogether one third (26) of the QTLs confirmed the map position and phenotypic effect of QTLs reported in the literature also detected in interspecific G. hirsutum × G. barbadense populations. Cases of colocalization of QTLs for different traits were more frequent than isolated positioning. Taking these QTL‐rich chromosomal regions into consideration, 19 regions on 15 different chromosomes, were identified as target regions for the marker‐assisted introgression strategy.

Background: Cotton blue disease (CBD), an important global cotton crop pathology responsible for major economic losses, is prevalent in the major cotton-producing states of Brazil. Typical CBD symptoms include stunting due to internodal shortening, leaf rolling, intense green foliage, and yellowing veins. Atypical CBD symptoms, including reddish and withered leaves, were also observed in Brazilian cotton fields in 2007. Recently, a Polerovirus named Cotton leafroll dwarf virus (CLRDV) was shown to be associated with CBD.

Partial virus genome sequence with high nucleotide identity to Cotton leafroll dwarf virus (CLRDV) was identified from two cotton (Gossypium hirsutum) samples from Thailand displaying typical cotton leaf roll disease symptoms. We developed and validated a PCR assay for the detection of CLRDV isolates from Thailand and Brazil.

Since 2006, Brazilian cotton (Gossypium hirsutum) crops planted with cultivars that are resistant to cotton blue disease have developed a new disease termed "atypical" cotton blue disease or atypical vein mosaic disease. Here, we describe the complete genomes of two virus isolates associated with this disease. The new virus isolates, called CLRDV-Acr3 and CLRDV-IMA2, were found to have a high degree of nucleotide and amino acid sequence similarity to previously described isolates of cotton leafroll dwarf virus, the causal agent of cotton blue disease. However, their P0 proteins were 86.1 % identical. These results show that this new disease is caused by a new CLRDV genotype that seems to have acquired the ability to overcome cotton blue disease resistance.