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What are molecular markers?
Any identifiable feature on the DNA sequence (for example, Single Nucleotide Polymorphisms (SNPs), Simple Sequence Repeats (SSRs) or Restriction Fragment Length Polymoprhisms (RFLPs)) that can be reliably assayed to detect genetic differences between individuals or populations.
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What are Single Nucleotide Polymorphisms (SNPs)?
Nucleotide positions along the chromosomes where the DNA sequences differ between individuals.
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What are Simple Sequence Repeats (SSRs)?
SSRs are tandem arrays of simple sequence repeats (mono, di, tri, tetra or penta- nucleotide motifs) in the DNA of eucharyotic organisms. SSRs represent a rapidly evolving (highly mutable) fraction of eucharyotic genomes. They are useful as genetic markers because differences in the length of the array (number of repeated motifs) can be easily assayed via PCR to identify genetic similarities and differences between individuals at specific loci.
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What is population structure?
A population is said to be structured if individuals do not mate at random (i.e., they deviate from Hardy Weinburger equilibrium). For example, individuals that are found in geographical proximity may be more likely to mate with one another than with individuals that are geographically distant from each other. Natural or artificial selection also contributes to non-random mating among members of a population.
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Why is the sub-population structure of rice important for breeding?
A majority of the world’s rice is produced from inbred (pure line) varieties and historically, inbred variety development has focused almost exclusively on crosses between members of the same sub- population (indica-indica) or between related sub-populations (i.e., tropical japonica x temperate japonica). This is largely due to the prevalence of sub-population incompatibilities that lead to sterility and make it difficult to obtain a random array of fertile recombinants from indica-japonica crosses.
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What are the problems associated with hybrid rice breeding?
In contrast to inbred rice variety development, hybrid rice breeding is more complicated, more costly and more technologically intensive. F1 hybrid seed that is sold to farmers is produced every year by crossing two, genetically different inbred lines; the parental inbreds are selected for crossing because they rise to highly productive, heterotic F1 hybrids. Because rice is a naturally inbreeding species, it is difficult to obtain high levels of out-crossing, due in large part to the enclosed floret morphology that helps to enforce the inbreeding habit. To encourage outcrossing, hybrid rice breeders use a male sterility system (generally either a two-line or the three-line system), but it remains challenging to achieve reliable and economically viable levels of out-crossing during F1 hybrid seed production.
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