Survival of the domesticated

“....the all-important part which selection by man has played, it becomes at once obvious, how it is that our domestic races show adaptation in their structure or in their habits to man's wants or fancies."
Charles Darwin (Origin of species)

Rice is one of the oldest cereals domesticated by man. Over centuries, rice varieties have been selected for increased yield, improved fertility, better adaptability of flowering time to local areas, and for having traits such as loss of seed color and loss of seed shattering. These constant selections have indeed resulted in varieties far superior to the ancestral stocks. But the ever inquisitive human mind likes to dissect what lies under these visible traits that brings about these changes that we aim for and are able to achieve.

In rice, seed shattering has a visible impact on the yield. A group of scientists have recently unraveled the molecular basis of this trait. Working with a hybrid population of a shattering type and a non shattering type cultivars of rice, Konishi et al (Science. 2006. 312: 1392-1396), identified 5 such regions on 5 different chromosomes of rice which contributed to decrease in seed shattering. These stretches of DNA which are associated with a particular trait are called Quantitative Trait Loci, or simply QTLs. QTLs are not necessarily genes but are a good start point to look for genes affecting a trait.

In this case, scientists identified one particular QTL which they called qSH1 (QTL of seed shattering in chromosome 1) of the non-shattering type rice cultivar as having the maximum affect on the reduction of seed shattering trait of rice. Near Isogenic Lines (NILs) are manipulated breeding lines such that they have a uniform genetic background of one parent, in this case the non-shattering rice cultivar, except that a given stretch of DNA which one is examining is from the other parent, that is the shattering rice cultivar in this case. In such NILs where the qSH1 was replaced by a stretch of DNA from the shattering type rice cultivars, scientists observed the formation of complete abscission layer between the seed and the pedicle of the rice grain. However the non-shattering lines with qSH1 showed complete lack of abscission layer formation, thus indicating that a mutation in qSH1 gene resulted in the loss of seed shattering in rice.

A Single Nucleotide Polymorphism (or difference), or SNP, at a specific position in qSH1 was the distinguishing feature between the shattering (had a ‘guanine’) and the non-shattering type (had a ‘ thyamine’) rice cultivars. Interestingly, qSH1 showed sequence similarity to a gene called REPLUMLESS (RPL) from Arabidopsis; a gene that has been shown to cause dehiscence in the fruit of this plant. This indicated an evolutionary conservation of this gene and in fact, the scientists did conclude by further experimentations that the RPL ortholog is indeed the qSH1 gene. The SNP between the shattering and the non-shattering rice cultivars seems to control the spatial mRNA expression of the qSH1at the abscission layer. The scientists believe that this gene may have other functions in the developmental process of rice.

Thus the loss of seed shattering observed in the selected cultivars of rice is caused by a mutation in the gene whose spatial control during development results in the observed trait. It is in such cases where a mutation which can cause serious defects in the development process of a species and wipe it off, that human intervention has played important role. Whereas low or no seed shattering would result in decreased propagation ultimately swiping away the species, from human standpoint it is a desirable trait as it would contribute to increased yield. The power of observation and selection has had its advantages and some disadvantages, which in this study was apparent when the scientists tried to obtain shattering related mutants. They realized that most rice cultivars have somehow lost the seed shattering habit. Scientist being what they are, found a way around this hurdle and carried on with their studies. But it does leave us with a thought that whereas selection has served us well over years, conservation of our natural wealth will keep us safe and prepared for the years to come.

“A high degree of variability is obviously favorable, as freely giving the materials for selection to work on………….But as variations manifestly useful or pleasing to man appear only occasionally, the chance of their appearance will be much increased by a large number of individuals being kept; and hence this comes to be of the highest importance to success.

Charles Darwin (Origin of species)