User:Mpatel61/sandbox

         The taxon Hordeum bulbosum is a perennial type of barley, and is in the Poaceae family. This family is known as the grass family. This barley is mostly found in the Western parts of the United States, Southern Europe, and in Australia. It is well known for its bright yellow color. Hordeum bulbosum grows optimally in high sunlight, neutral pH’s, and in moist soil and the pH range is from 6.0 to 8.0. It grows best in moist soil, however it can also survive in dry soil and this is one of the reasons this species has thrived for so long. Thus its habitat includes wet meadows, dry hillsides, and unrestrained fields. When grown in optimal conditions, it can grow up to five feet tall. This barley is in plant form from June to July, due to the high volume of sunlight obtained by the plant. Another interesting aspect that is seen, is that the flowers have male parts and female parts; this is known as a hermaphrodite. Because of this feature, the Hordeum bulbosum barley can produce both male and female gametes. This barley, like all species in the grass family are immobile and they rely on the wind for pollination to occur. 

         Much research has been done on Hordeum bulbosum in order to find ways to improve traits by artificial selection. One way this has occurred is by looking at the introgression lines of this species. After figuring out what on what chromatin introgression has occurred, from the undomesticated species, researchers were able to genetically locate the lines of EST-derived PCR markers. Over 35% of the genetic map has been complete and it has assisted barley researchers in improving this taxon. 

         This diploid species has also undergone whole-genome shotgun assembly, however it has not been completed due to the sheer size of the barley genome, which is 5 Gb. The shotgun sequencing works by creating shorter strands of DNA, and these strands are overlapped and then put into one sequence by a computer. This allowed the full genome to be sequenced and this method can be used to compare cultivated barley and its related species. Studying these sequences helps provide a better understanding of the variation that resides in the barley genome and how this variation can be improved in the future.

         The survival of this barley genome has been due to it’s ability to thrive in harsh conditions and because of resistance genes. One of these resistance genes is Rph22, and it was introgressed from Hordeum bulbosum to cultivated barley. With the use of molecular markers, researchers found that this gene covers about 20% of the entire chromosome. The resistance gene worked by increasing the latency period of the leaf rust fungus and this aided the barley due to a decrease in the infection frequency. The resistance locus was found to be on the distal portion of the introgression and flanking markers were used to reduce the linkage drag. This research combined with research on other resistance genes in barley helps breeders and researchers to improve various types of barley.

The species bulbosum from the genus hordeum, is known to use a large number of retrotransposons in their genome that is derived from rye. By cross referencing different marker sequences there were many sequences similar between the hordeum bulbosum and barley genotypes.

The H. bulbosum is a diploid taxon, but sometimes can be polyploidy. Using whole-genome sequencing the parents of the bulbosum species can be found, which were a mixture of hexaploidy and diploidy. The nuclear gene disrupted meiotic DNA and is a theory of why the diploid occurred.

Whole-genome shotgun sequencing has allowed for single genes to be analyzed in detail. With having RNA sequences as well, this provides reproducible targeted exons to study cultivated barley and it's differences from ancestral barley. Natural variation can be understood and the large amount of genetic diversity in the Hordeum genus can be identified.

The Hordeum bulbosum introgression on chromosome 2, introgressed from a non-host species and was later converted to cultivated barley. This introgression contains a high number of resistance genes to fungus, which assists the bulbosum species in surviving. Flanking markers also were a factor that helped in noticing the resistance locus of the gene.

The chromosome arm length of the Hordeum genus have been found to be correlated with recombinant lines. The chromosome arms are found to be shorter in the more recombinant lines. Hybrids of the Hordeum genus are similar to the bulbosum chromosome associations.

By understanding the DNA sequences in the Hordeum genus, many areas of the genome has been artificially selected for improvement. The recombination frequencies in the areas of introgression have been found to have desirable traits. By using genotype-by-sequencing the molecular marker development will improve for barley breeding.