Genetics of ‘off type’ plants in seed multiplication plots of cotton (Gossypium hirsutum L.)

This blog is about how to interpret the appearance of ‘off type’ plants in foundation seed progenies, regardless of the 100% purity in the breeder seed plots

Breeder seed is the base source for the quality hybrid seed production in cotton or for any crops. Foundation seeds are multiplied from breeder seed  and used as the source seed for the certified seed production. To maintain the higher genetic purity standards at the certified seeds, the genetic purity of breeder seed  is very important.

Despite of the genetic purity and uniformity of plants at breeder seed, at rare instances there is a distortion of genetic purity at the foundation seed multiplication plots. There will be a chance for two kinds of 'off type' plants that  appears in foundation plots.

1. Plants of different variety of same species. This is due to admixture of seeds during seed processing steps and can be eliminated by stringent quality control checks.
2. Plants of same variety of same species with one or two DUS characters altered. This kind of off types are more interesting to breeders since those plants are not appeared on the breeder seed plot. Based on the DUS character altered and proportion of such off type plants, breeder might able to give a genetic explanation for the deviation of purity

Here we will investigate the situations in which, ithe breeder seed plot is morphologically 100% pure, but segregation and appearance of off types at foundation field arises. Based on the proportion of the off type plants, the genetic cause can be explained. We are not taking account of admixture plants into our discussion, because the occurrence of admixture is purely on physical means, and no genetics involved.

1.) 10% off type plants (10/100) plants with altered DUS characters

This is very rare situation, arises due to segregation at large loci in some of the plants. For some breeding lines the fixation of homozygosity takes more generations of selfing. Though the progenies of breeding lines looks homogenous, some plants might still be heterozygous at some loci. When such lines are advanced to breeder seed multiplication, (owing to the commercial success of the hybrid) the heterozygous plants escapes detection. When advanced to foundation seed multiplication, some plants appear as distinct from the original parent. The escape  from breeder seed plot is  due to heterozygous and dominanace of genes. During the pollination at breeder seed multiplication, selfing occurs at great extend, leads to fixation of some  genes in the progenies of the heterozygous plants. The genotype of the progenies is now distinct from the original parent and appears as ‘off type’ in the foundation field.

2.) 1 % of off type plants (1/100) plants with altered DUS characters

In cotton, some of the DUS characters like petal colour, pollen colous are coded by single major genes. The alleles of the gene has alternate phenotypes. If the trait is encoded by a dominant gene, the homozygous and the heterozygous plants will express one phenotype and the recessive plants will express the alternate phenotype. If the breeder seed plot is rich in heterozygous, and dominant homozygote plants, all the plants will be phenotypically similar. The heterozygous plants segregates and produces recessive genotype progenies, that appears as alternate ‘off type” at foundation fields.

3.) 0.1% of off type plants (1/1000) plants with altered DUS characters

The above explanation holds true for this proportion of plants, except the fact that initial load of heterozygous plants at breeder seed plots will be lesser than above case. If there are one  or few heterozygous plants at breeder seed plots, this will lead to production of 0.1% of plants with recessive phenotype.

4.) 0.01% of plants (1/10,000) plants with altered DUS characters

So far heterozygosity can be accounted for the production of off type plants. But Hetorozygosity cannot explain the appearance of 0.01% of ‘off type’ plants because, a single heterozygous plant is enough to produce 0.1% of off type plants at foundation stage. Even if the breeder seed plot is 100% genetically pure, the appearance of such proportions of off types are possible and needs an investigation. In cotton, the appearance of 1/10,000 plants off types can be attributed to natural out crossing by honey bees or other insect pollinators. The out crossed plants will be of intermediate phenotype, carries few altered DUS trait. Hutmacher (2006) pointed out that 0.04% of out crossing occurs at up to 1500 distance with insect pollinators in cotton commercial fields. The cotton pollen is heavy and sticky in nature and out crossing through wind never exceeds  more than few meters

5.) 0.001% of plants (1/1,00,000) plants with altered DUS characters

Insect pollination can also explain 0.001% of plants could be the result of out crossing. The out crossed plants appear as intermediate phenotype of original parent and the pollen donar.  In very rare instance, the off type plants are same as original parents, except for the one DUS character differ from original parent. Classical genetics cannot explain appearance of such type plants at this 0.001% proportions. In the absence of segregation and outcrossing,  the appearance of 1/10, 00,000  off type plants can be explained by the population genetics

The seed multiplication plot in isolation is equivalent to population of random mating individuals. According to the Hardy Weinberg law, In a random mating population, the gene and the genotype frequencies are remain constant through generation to generations, unless selection, migration or mutation operates on the population. In a breeder seed multiplication plots no selection is practiced since all plants are homogenous and homozygous. The isolation distances eliminate the possibility of population migration through out crossing. Mutation could be the only agent acting on the seed multiplication population. The average mutation rate of living organism is 1/10, 00,000 per gene per gamete. Thus, one out 10, 00,000 pollens will carry a mutation in any one of the gene. A single cotton flower produces 30,000 pollens. Therefore one pollen in every three flowers might carry a mutation in a gene. But most of the mutated genes does not code for visible phenotype and undetectable at progenies. If the mutation occurs at the genes codes for the any one of the DUS characters, the mutation can be detected in the progenies as off types, at the proportions 1/10,00,000 to 1/1,00,00,000.