Browsing by Author "Simpson, Charles E."
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Item A Proof-of-Principle Study of Non-invasive Identification of Peanut Genotypes and Nematode Resistance Using Raman Spectroscopy(2022) Payne, William Z.; Dou, Tianyi; Cason, John M.; Simpson, Charles E.; McCutchen, Bill; Burow, Mark D. (TTU); Kurouski, DmitryIdentification of peanut cultivars for distinct phenotypic or genotypic traits whether using visual characterization or laboratory analysis requires substantial expertise, time, and resources. A less subjective and more precise method is needed for identification of peanut germplasm throughout the value chain. In this proof-of-principle study, the accuracy of Raman spectroscopy (RS), a non-invasive, non-destructive technique, in peanut phenotyping and identification is explored. We show that RS can be used for highly accurate peanut phenotyping via surface scans of peanut leaves and the resulting chemometric analysis: On average 94% accuracy in identification of peanut cultivars and breeding lines was achieved. Our results also suggest that RS can be used for highly accurate determination of nematode resistance and susceptibility of those breeding lines and cultivars. Specifically, nematode-resistant peanut cultivars can be identified with 92% accuracy, whereas susceptible breeding lines were identified with 81% accuracy. Finally, RS revealed substantial differences in biochemical composition between resistant and susceptible peanut cultivars. We found that resistant cultivars exhibit substantially higher carotenoid content compared to the susceptible breeding lines. The results of this study show that RS can be used for quick, accurate, and non-invasive identification of genotype, nematode resistance, and nutrient content. Armed with this knowledge, the peanut industry can utilize Raman spectroscopy for expedited breeding to increase yields, nutrition, and maintaining purity levels of cultivars following release.Item Comparisons of de novo transcriptome assemblers in diploid and polyploid species using peanut (Arachis spp.) RNA-Seq data(2014) Chopra, Ratan (TTU); Burow, Gloria; Farmer, Andrew; Mudge, Joann; Simpson, Charles E.; Burow, Mark D. (TTU)The narrow genetic base and limited genetic information on Arachis species have hindered the process of marker-assisted selection of peanut cultivars. However, recent developments in sequencing technologies have expanded opportunities to exploit genetic resources, and at lower cost. To use the genetic information for Arachis species available at the transcriptome level, it is important to have a good quality reference transcriptome. The available Tifrunner 454 FLEX transcriptome sequences have an assembly with 37,000 contigs and low N50 values of 500-751bp. Therefore, we generated de novo transcriptome assemblies, with about 38 million reads in the tetraploid cultivar OLin, and 16 million reads in each of the diploids, A. duranensis K38901 and A. ipaënsis KGBSPSc30076 using three different de novo assemblers, Trinity, SOAPdenovo-Trans and TransAByss. All these assemblers can use single kmer analysis, and the latter two also permit multiple kmer analysis. Assemblies generated for all three samples had N50 values ranging from 1278-1641 bp in Arachis hypogaea (AABB), 1401-1492 bp in Arachis duranensis (AA), and 1107-1342 bp in Arachis ipaënsis (BB). Comparison with legume ESTs and protein databases suggests that assemblies generated had more than 40% full length transcripts with good continuity. Also, on mapping the raw reads to each of the assemblies generated, Trinity had a high success rate in assembling sequences compared to both TransAByss and SOAPdenovo-Trans. De novo assembly of OLin had a greater number of contigs (67,098) and longer contig length (N50=1,641) compared to the Tifrunner TSA. Despite having shorter read length (2 × 50) than the Tifrunner 454FLEX TSA, de novo assembly of OLin proved superior in comparison. Assemblies generated to represent different genome combinations may serve as a valuable resource for the peanut research community.Item Evaluation and selection of interspecific lines of groundnut (Arachis hypogaea l.) for resistance to leaf spot disease and for yield improvement(2021) Denwar, Nicholas N. (TTU); Simpson, Charles E.; Starr, James L.; Wheeler, Terry A.; Burow, Mark D. (TTU)Early and late leaf spot are two devastating diseases of peanut (Arachis hypogaea L.) worldwide. The development of a fertile, cross-compatible synthetic amphidiploid, TxAG-6 ([A. batizocoi x (A. cardenasii x A. diogoi)]4x ), opened novel opportunities for the introgression of wild alleles for disease and pest resistance into commercial cultivars. Twenty-seven interspecific lines selected from prior evaluation of an advanced backcross population were evaluated for resistance to early and late leaf spot, and for yield in two locations in Ghana in 2006 and 2007. Several interspecific lines had early leaf spot scores significantly lower than the susceptible parent, indicating that resistance to leaf spot had been successfully introgressed and retained after three cycles of backcrossing. Time to appearance of early leaf spot symptoms was less in the introgression lines than in susceptible check cultivars, but the opposite was true for late leaf spot. Selected lines from families 43-08, 43-09, 50-04, and 60-02 had significantly reduced leaf spot scores, while lines from families 43-09, 44-10, and 63-06 had high pod yields. One line combined both resistance to leaf spot and high pod yield, and several other useful lines were also identified. Results suggest that it is possible to break linkage drag for low yield that accompanies resistance. However, results also suggest that resistance was diluted in many of the breeding lines, likely a result of the multigenic nature of resistance. Future QTL analysis may be useful to identify alleles for resistance and allow recombination and pyramiding of resistance alleles while reducing linkage drag.Item Genetic mapping of leafspot resistant QTLs, and introgression into West African adapted and US-high oleic peanuts(2018-08) Tengey, Theophilus K.; Mendu, Venugopal; Burow, Mark D.; Woodward, Jason E.; Simpson, Charles E.; Denwar, Nicholas N.; Akromah, RichardLeaf spot disease is a very important disease in Ghana and the US. Breeding for resistance to this disease is difficult as it is controlled by many recessive genes. Wild species have been identified to habor resistant genes to leafspot disease but the differences in their genomes compared to cultivated species makes trait transfer difficult. The development of TxAG-6 through the cross [A. batizocoi x (A. cardenasii x A. diogoi)]4x has helped to circumvent this drudgery in breeding. Leaf spot disease resistance have been identified in BC3 populations of a cross between Florunner and TxAG-6. RFLP and SSR genetic linkage maps of this population have also been constructed in order to map QTLs of disease resistant from this population. RFLPs are not ideal markers because of slow turnaround time, need for large amounts of DNA, and use of radioactivity. Although SSRs have been preferred over RFLPs, genotyping with SSRs is also quite laborious, making Single Nucleotide Polymorphisms (SNPs), the markers of choice in genotyping. In this study a SNP based genetic linkage map has been constructed for the BC1 population of which markers have been used to genotype 317 BC3 individuals. These were used in conjunction with leaf spot data collated from Ghana, Burkina Faso and US in identifying leaf spot resistant QTLs. QTLs for Early and Late leaf spot have been identified. Crosses were also made to transfer leaf spot resistant genes from BC3 lines into Spanish peanut varieties in West Africa and the US. These materials were advanced to the F3 stage and evaluation for leaf spot disease done in Ghana. Several lines have been identified to be resistant to leaf spot disease, selected materials will be advanced further and subsequently released as leaf spot resistant materials in the future.Item Identification of Single Nucleotide Polymorphisms (SNPs) in Arachis (Peanut) Wild Species and Cultivated Accessions by Solexa Transcriptome Sequencing and Utilization of SNPs for Linkage Mapping in an Arachis A Genome Diploid F2 Population(2014-12-09) Chopra, Ratan; Burow, Mark D.; Sharma, Jyotsna; Payton, Paxton; Simpson, Charles E.; Mudge, JoannWe report the utilization of de novo assembly for tetraploid and diploid peanut to achieve optimal quality transcriptome references using three different assemblers – Trinity, TransAByss and SOAPdenovo-trans. Results of de novo assembly were used to carry out SNP identification in a panel of twenty two accessions of the Arachis genus, including cultivars representing Arachis hypogaea subsp. hypogaea - var. hypogaea, var. hirsuta, and Arachis hypogaea subsp. fastigiata - var. fastigiata, var. vulgaris, var. peruviana, and var. aequtoriana, and wild species representing the A-, B-, and K- genomes, a wild tetraploid – Arachis monticola, and a synthetic amphidiploid - TxAG-6. SNPs identified in the panel provided an insight into the extent of transcript polymorphism present in the genus. Expression analysis performed on three allopolyploids with their ancestral diploid genome donors indicated that B-genome transcripts of the tetraploids were expressed in a pattern more closely related to the B- genome diploids. Validation of SNP calls was performed using allele-specific chemistry on a LightCycler 480. Polymorphic SNPs between A. duranensis x A. cardenasii from the above dataset were used to develop a genetic map on LightCycler 480 and on a high-throughput genotyping platform the Fluidigm Biomark HD. A total of 31 QTLs using composite interval mapping were identified for ten plant architectural traits such as leaf measurements, main stem height, presence of main stem flowers, and seed weight. In summary, this study generated a transcriptome resource for twenty-two peanut accessions and provided an insight into transcript variability in peanut accessions. Also, the genetic map and QTL studies provide a base to assist future utilization of the transcript-based SNPs in peanut.Item Use of targeted amplicon sequencing in peanut to generate allele information on allotetraploid sub-genomes(2020) Kulkarni, Roshan (TTU); Chopra, Ratan; Chagoya, Jennifer; Simpson, Charles E.; Baring, Michael R.; Hillhouse, Andrew; Puppala, Naveen; Chamberlin, Kelly; Burow, Mark D. (TTU)The use of molecular markers in plant breeding has become a routine practice, but the cost per accession can be a hindrance to the routine use of Quantitative Trait Loci (QTL) identification in breeding programs. In this study, we demonstrate the use of targeted re-sequencing as a proof of concept of a cost-effective approach to retrieve highly informative allele information, as well as develop a bioinformatics strategy to capture the genome-specific information of a polyploid species. SNPs were identified from alignment of raw transcriptome reads (2 × 50 bp) to a synthetic tetraploid genome using BWA followed by a GATK pipeline. Regions containing high polymorphic SNPs in both A genome and B genomes were selected as targets for the resequencing study. Targets were amplified using multiplex PCR followed by sequencing on an Illumina HiSeq. Eighty-one percent of the SNP calls in diploids and 68% of the SNP calls in tetraploids were confirmed. These results were also confirmed by KASP validation. Based on this study, we find that targeted resequencing technologies have potential for obtaining maximum allele information in allopolyploids at reduced cost.