Based on the results obtained from this study, it is apparent that intended aim was attained. In the initial stages, 992, 682 gene variations identified from the 17 bean varieties once sequencing had occurred. Linkage maps with up to 7,040 markers were also obtained, resulting in 432.2Mb of sequence fastened to develop Phaseolus vulgaris v1.O. Also, a set of 6000 SNPs was also selected after genotyping 365 bean varieties along with 134 snap accessions of beans.
DNA molecular markers are very essential since they are utilized in the development of linkage maps in almost all the major crop varieties. This research was conducted for a variety of reasons; all of which were attained in the final analysis. One involves the identification of SNPs which exhibited high Polymorphism. Secondly, the research was meant to develop genetic linkage maps. It was also, purposed towards the anchorage of common bean DNA sequences.
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Delving into the materials and methods utilized in the study, it is evident that the GoldenGate assay play a significant role. This involved 1,307 SNPs which were utilized when identifying gene sequencing among the 192 bean genotypes identified for the study; after which 15 varieties were acknowledged for throughput sequencing. Jalo EEP558 and BAT93 were also utilized.
In the course of sequencing, 17 common bean varieties were pulled out from the seeds. The next step involved the selection of 6bp long sequences that were later impleaded to fragments with sizes of between 350 and 800bp. Some software such as Off-line Basecaller and CASAVA (v 1.7) were employed in the course of mapping.
`Further still, Putative SNPs or gene varieties were assessed based on the Illumina`s Assay Design Tool. In the process, SNPs that held a score that was less than 0.6 ended up being eliminated. In the optimization of polymorphism, BARCBEAN6K were used to distinguish between the varieties of market classes in place. It is also important to note that BARCBEAN6K_2 which is also a common BeadChip was assembled from the v0.9 assembly of gene sequencing. Gene varieties were also selected with an aim of anchoring scaffolds.
It is evident that no questions were left unanswered at the end of the study. To further validate this, and for it to be possible to establish successful SNP calls, 17 bean varieties were utilized and also genotyped using BeadChips. Also, in the course of validation, 90% and 92% of the 6000 SNPs were included in the BARCBean6K_1 and BARCBean6K_2 Bead pool respectively. MAF which was greater than 10% of the bean varieties was observed in 95% of the SNPs. Further still, the BARCBean6K_2 and BARCBean6K_1 were used to map 267 F 2 plants using the Red Hawk and Stampede beans. Besides, the JoinMap 4.0 also played a critical role in the development of linkage maps.
The BARCBean6K_3 BeadChip was later developed from 132 snap bean and 365 bean accessions. It was also observed that the bean varieties in this case were more polymorphic in the related market class. This ensured that the linkage maps were enabled for preferential selection in heterochromatic areas exhibiting low rates of recombination, which in turn ensured that the SNPs were reduced significantly.
Up to 286.7 million reads were developed from the DNA of the 17 varieties of beans under this study. In addition to this, the CASSAVA 1.7 software made it possible for the experiment to identify up to 1, 857, 237 gene varieties(SNPs), by checking on the alignment of 14x genome sequence. This amounts to an equivalence of 3SNPS for each kb genome-wide. The 992,682 remaining gene variations were utilized in the development of BARCBean6K_1 and the BARCBean6K_2 Bead Chips.
Finally, in the course of constructing bean linkage map, 262 F 2 plants from Red Hawk and Stampede were used. Also, loci bearing significant segregation was eliminated from the SNPs. Besides, 6531 SNPs ended up being reserved for the linkage process. It has also been established that diversity amongst the various gene varieties of beans is limited. This results from the disparities in the agrological and morphological states amongst other characteristics. In this case, development of polymorphic markers within each race is imperative to ascertain diversity and further research on various gene types.
