Rajesh S Patil What about AFLP? AFLP should produce more polymorphism than SSR.

Yuan-Yeu Yau Thanks for the suggestion. But expression of QTLs may not be known with AFLP. I have never used AFLP. This has set me thinking.

Rajesh S Patil Is color in the cotton lint a QTL trait? Has that been studied and proved?

Yuan-Yeu Yau , Thanks for the interest shown. Sir, Colour shows a graded response from dark brown to medium to light. We are suspecting all sorts of gene action and GxE interaction also. There are no studies to support us or otherwise. It is a challenge. We tried isolating the pigments causing colour and we are yet to succeed. Staining techniques pointing towards epigenetics have been successful. Chi square tests in F2 of different populations has given different interactions as well as simple 3:1 ratio also. All this was my PhD student's work. After all this we are yet to get the transcriptome study results. The ultimate aim is to identify color-causing genes and put them in white lint genotypes with exceptional fibre properties as the present colour genotypes do not have very good fibre. Having seen this, I thought I need to be careful about the techniques to be used while handling the next concept of earliness.

Rajesh S Patil How did you do this? Cotton is a selfing plant species. So, you can see the lint colors are with different hue form different bolls in the same plant (due to epigenetic?)?

Have you seen this paper below. The possible molecular mechanisms causing different shades in colored cotton (ex. brown color has 8 shades).

" Various shades of lint appeared in the F 1 progenies and the inheritance of lint colors appeared to be controlled by dominant genes with varying degrees of dominance. There was also some indication for the involvement of maternal effects in the manifestation of lint colors. "

https://www.tandfonline.com/doi/full/10.1080/11263500903178158?needAccess=true

Another paper, from this paper it says the cause of different shades of brown color is due to a SINGLE gene, which is Partial Dominant to white gene. "

"We crossed wild G. barbadense accessions and G. hirsutum cultivars (with white fiber) and obtained the F2 generations, and BC1 and BC2 backcrosses. It may be concluded that fiber color is controlled by one gene, with partial dominance of the brown color over white."

Yuan-Yeu Yau Thanks a lot for the references. We indeed have quoted the paper mentioned. Our findings were as below

Inheritance of brown fiber colour

To study the inheritance of fiber colour in G hirsutum two separate crosses were attempted by crossing Dark brown genotype (DB 39) with Sahana and ARBH 813 with Dark brown genotype (DB 41). The F1 obtained had intermediate lint colour in both cases. The F2 seeds obtained from selfing F1 were raised and the variation observed in the F2 population was very high, representing different shades of lint colour.

The number of plants in the cross ARBH 813 with Dark Brown had 239 pigmented and 48 non-pigmented plants and the cross Dark Brown with Sahana showed 142 pigmented and 31 non-pigmented plants. The F1 generations of both crosses had an intermediate color indicates that the brown fiber partially dominant over the white. The F2 generations showed plant segregation of colored fiber and white fiber well fitted to the segregation of colored fiber and white fiber well fitted to the expected 15:1 proportion according to the χ2 test.

Inheritance of almond fiber colour

In diploid cotton the number of plants in cross DDCC1 with DLSa 17 had 139 pigmented and 29 non pigmented plants as presented in Table1. The F1 plants had almond color indicates that almond color is dominant over the white. The F2 population fitted to the expected 3:1 proportion according to the χ2 test.

Inheritance of green fiber colour

Inheritance of the green fiber trait was assessed based on both F2 and backcross generations generated between intra-hirsutum and inter-specific crosses. In Intra-hirsutum cross had 49 pigmented fiber and 131 non-pigmented fiber. In inter specific cross between hirsutum and barbadense 167 plants white linted and 54 plants had green fiber. It has been seen that one gene controls the expression of the green fiber since the segregation exhibited in the F2 fit perfectly with 3:1 ratio.

The F1s of Dark brown and green was derived from the parents contrasting for fiber colour, fuzz of seed is green whereas the fiber is brown. Brown is partially dominant over the green fiber. The F2 segregants showed brown fiber and green fiber is well fitted to the expected ratio in 3:1 ratio. There were varying shades of brown green and mixed pattern of fiber was observed and it limits the ease of phenotyping in this case.

F2 populations indicated the presence of gene interaction which reveals that fiber colour development is controlled by a pair of genes with duplicate epistasis (15:1) for brown fiber. The variation observed for fiber colour was not discrete and continuous. There were varying shades of brown which need to be further investigated. The F2 segregation ratio 15:1 holds good if only colour linted and white linted classes are considered irrespective of variation in lint colour. Thus it indicates that brown colour of lint is mainly controlled by two incompletely dominant genes with probable presence of some modifiers and intensifiers. Inheritance pattern of almond fiber colour in Gossypium arboreum is partially dominant over white and it is under the control of singe gene with biallelic nature. In intraspecific and interspecific crosses of green linted fiber with white lint white is dominant over green and inherited as monogenic trait with two alleles. In dark brown and green linted cross brown is dominant over white and shows typical incomplete dominance.

For studying such a complex trait we need to handle large populations, development and standardization of specific protocols using colorimetric methods. Fiber colour is a diagnostic trait for identifying duplicate accessions in germplasm, maintaining the identity of accession, identification of true hybrids, establishing distinctness, uniformity and stability of cultivar, a pre requisite for protecting intellectual property rights associated with the cultivar development. Understanding of genetics of fiber colour will helps the plant breeder transfer/ pyramiding of different fiber colour trait in the background of agronomically superior genotype.