- New software features for GWAS in polyploids - presented by Jeffrey Endelman: This presentation will cover new features added to GWASpoly in 2021, including (1) partial R2 values, (2) mixed ploidy datasets, and (3) VCF files as input.
- Novel Genomic Resources Enable Association Mapping in Tetraploid Blackberry - presented by Mason Chizk et al.
Mason Chizk1, Margaret Worthington1, Carmen Johns1, Carly Godwin1, John R. Clark1, Rishi Aryal2, and Hamid Ashrafi2. 1University of Arkansas, Fayetteville, AR. 2North Carolina State University, Raleigh, NC.
Until recently, large-scale association mapping studies in autopolyploid crop species have been impractical due to cost of sequencing with adequate read-depth, computing limitations, and software availability. In a collaborative effort that leverages targeted next-generation sequencing (NGS) technologies and newly available software packages to overcome these obstacles, we report the first genome-wide association study (GWAS) in autotetraploid blackberry (Rubus L. subgenus Rubus Watson), identifying numerous quantitative trait loci (QTL) for potential use in marker-assisted selection (MAS). Using NGS via the Capture-Seq platform, 35,054 well-distributed probes were designed from the ‘Hillquist’ (Rubus argutus Link.) reference genome. From 2019 to 2021, a panel of 307 commercially available fresh-market blackberry cultivars and University of Arkansas Division of Agriculture breeding selections were sequenced and phenotyped for an array of traits that encompass fruit morphology, postharvest texture, acidity, sweetness, seed traits, thorniness, and plant height. Using the designed probe set, 81,150 high-quality single nucleotide polymorphisms (SNPs) were identified with greater than 150x average read-depth. Through phenotypic analyses, high broad-sense heritabilities exceeding 0.75 were observed for multiple quantitative traits including primocane height, thorn density, fruit weight, fruit length, drupelet number, 100-seed weight, and seed width/length ratio. QTL were identified for all for each of these traits except fruit weight. A QTL for fruit firmness was identified on Ra04, less than 0.5 Mb away from two polygalacturonase (PG) homologs and two pectin methylesterase (PME) homologs. Homologs for both candidate genes have been widely implicated in texture variation for other crops. A shared QTL for titratable acidity (TA) and pH was identified on Ra05 near three malate synthases, two vacuolar malate transporters, one MYB transcription factor, and one phosphoenolpyruvate carboxylase PEPC. Other major QTL associated with primocane height and thornlessness were discovered on chromosome Ra04 at 25 and 33 Mb, respectively. These data will not only be used to design the first diagnostic markers for MAS in blackberry, but will serve as a foundational training dataset for genomic selection to achieve gains in heritable traits with few to no high-impact QTL, such as soluble solid content (SSC) and fruit weight.
- Evaluation of Musa Accessions Indigenous to Benin Republic for Resistance to Black Sigatoka Disease - presented by Nweze Nwabueze Peter et al.
Nweze Nwabueze Peter1, Enoch G. Achigan-Dako2, Celestine Azubuike Afiukwa1, and Happiness O. Oselebe1. 1Ebonyi State University, Nigeria. 2University of Abomey Calavi, Benin Republic.
Black sigatoka disease caused by Pseudocercospora fijiensis is the most destructive disease of Musa species. The aim of this study was to identify Musa accessions cultivated in Benin Republic that possess host resistance capacity to black sigatoka disease. A total of 72 Musa accessions were used in the study including 58 local accessions and 14 accessions from International Musa Transit Centre (ITC) in Belgium. The experiment was laid out using the Augmented Split Plot Design at Misserete, in Benin Republic. Agronomic data were collected 9 months after planting according to standard evaluation method for the disease including; symptom appearance (SA, in days), rate of leaf death (%LD), youngest leaf spotted (YLS), number of standing leaves (NSL), index of non-spotted leaf (INSL), area under disease progress curve (AUDPC) and disease severity index (DSI). The presence of genes for black sigatoka resistance (bs1) was evaluated using a gene specific SSR marker and one unspecified disease resistant gene (UDRG) in Musa. DNA sequencing was done using ABI sequencer. The results revealed high significant difference (p<0.0001) in sigatoka disease incidence and severity among the accessions with the rate of symptom appearance (SA) ranging from 10 to 36 days, NSL and YLS ranged from 3.0 to 14.0 and 2.0 to 6.0 respectively, while the values of INSL, DSI and AUDPC ranged from 12.5 to 60.0, 13.33 to 52.0 and 58.0 to 239.0, respectively. A dendogram based on disease sensitivity data showed 3 distinct clusters (A-C). cluster A contains 20 resistant accessions, cluster B is made up of 16 susceptible accessions, while cluster C includes 36 intermediate resistant accessions. Also, the dendogram of the amplified resistance gene sequences and the gel matrix also clustered the Musa accessions into 3 groups which showed a little variation with from their morphological pattern of resistance to the disease. Multiple sequence alignment result based on UDRG sequences showed missing nucleotide sequence in some susceptible accession. The marker-trait association analysis revealed a mutual occurrence between UDRG_300 and the morphological indicators of resistance to the disease (YSL, NSL and INSL). The study therefore identified black sigatoka resistant Musa accessions among Benin Republic cultivars and provided a genetic tool (UDRG_300) which can be exploited for improvement of the crop for sigatoka disease resistance.
Joao Nomura1, Moctar Kante2, Elisa Salas2, Hannele Lindqvist-Kreuze2, Fernando Angelo Piotto1, and Jeffrey Endelman3. !Escola Superior de Agricultura Luiz de Queiroz, Sao Paulo, Brazil. 2International Potato Center, Lima, Peru. 3University of Wisconsin - Madison, Madison, WI.
Potato is one of the most important crops for humans, especially in developing countries. Extreme climate events are becoming more frequent, and drought is one of the abiotic stresses that can severely impact yield. To understand the genetic response for drought tolerance in potato, 655 clones were evaluated at two semi-arid, lowland sites in Peru. All clones were evaluated under full and deficit irrigation at both sites. Water reduction in the deficit treatment began when 5% of the plants started to flower, which is a morphological sign of tuber initiation. The interval between irrigation events in the full treatment was 2-3 days vs. 15 days in the deficit treatment. Targeted amplicon sequencing (DArTag) was used for genotyping, which generated 2244 SNPs after quality control. Genotype calls were made using the R/updog package, and quantitative genetic analyses used the R/StageWise package. The mean yield under full vs. deficit irrigation was 533 vs. 204 g plant-1, which represents a yield loss of 62%. Across the panel of 655 clones, the yield reduction ranged from 42 – 84%. No marker-trait association was detected for yield under full irrigation, but under deficit irrigation we observed a GWAS peak at the beginning of chromosome 5 that accounted for R2 = 21% of the breeding value. This region corresponds to the location of CDF1, a well-known gene affecting potato maturity, and which more recently has been implicated in water homeostasis. When yield under drought was plotted against the visual ratings of vine maturity, there was a tendency for earlier clones to yield more than late clones. The average yield under drought increased by 21.5 g plant-1 per allele dose at the marker linked to CDF1. Even though drought tolerance is likely affected by many genes, CDF1 appears to be an important target for genetic improvement of this trait.
Ao Jiao1, Sanjeev Gautam1, Jeewan Pandey1, Douglas C. Scheuring2, Jeffrey Koym1, and M. Isabel Vales1. 1Department of Horticultural Sciences, Texas A&M University, College Station, TX. 2Texas A&M AgriLife Research and Extension Center, Lubbock, TX.
Potato tuber dormancy is defined as the period after harvest during which tubers do not sprout even under favorable conditions. The length of the dormancy period is measured from vine kill until tubers start sprouting and it is affected by genotype and environmental factors. Premature dormancy break is a major factor causing post-harvest tuber quality reduction. Common methods to prevent sprouting include cold storage and the use of sprout inhibitors. Cold storage causes cold-induced sweetening and results in higher energy costs, whereas sprout inhibitors raise health and environmental concerns. Developing potato varieties with long dormancy could contribute to reducing the use of cold storage and sprout inhibitors. In this study, we evaluated tuber dormancy variation and investigated the genetic background of tuber dormancy. Over 200 clones from the Texas A&M Potato Breeding Program were grown in Dalhart, TX in 2019 and were evaluated for dormancy at room conditions (18 °C, RH 60%, dark). The clones exhibited variation in dormancy ranging from 38 to 155 days, with the Russets having significantly longer dormancy (> 96 days) than other market groups (70 – 80 days). Two Texas A&M varieties, Reveille Russet and Vanguard Russet, were among the clones with the longest dormancy. A genome-wide association study was performed using GWASpoly with Infinium Illumina 22K V3 Potato Array to identify genomic regions associated with tuber dormancy. The main QTL identified was on chromosome 9, explaining 11% of the phenotypic variation. Follow-up evaluations will be conducted at additional locations under room temperature and cold storage.
- Genome-Wide Association Study on Potato Tuber Defects Under Heat Stress - presented by Sanjeev Gautam and Isabel Vales
Sanjeev Gautam and M. Isabel Vales. Department of Horticultural Sciences, Texas A&M University, College Station, TX. Texas A&M AgriLife Research and Extension Center, Lubbock, TX.
Heat stress reduces marketable tuber yield and quality of potatoes. Tuber defects can be external (heat sprouts, chained tubers, knobs) or internal (vascular discoloration, internal heat necrosis). Successful cultivation of potatoes under heat stress requires planting heat-tolerant varieties that can produce high yields of marketable tubers. Heat tolerance is a complex trait and breeding for it possesses several bottlenecks. To facilitate future marker-assisted selection for heat tolerance, a genome-wide association study (GWAS) aimed to identify genomic regions associated with heat tolerance was conducted. Phenotyping for a panel of 217 diverse potato genotypes was conducted near Springlake, Texas (heat stress location) for two years using a randomized complete block design with two replicates. The genotypes differed in their capacity of expressing the external as well as internal defects on tubers under heat stress. GWAS was conducted using GWASpoly with Infinium Illumina 22 K V3 Potato Array. Significantly associated SNPs with external defect traits were located on chromosomes 3, 4, 6, and 7 while those with internal defect traits were located on chromosomes 3 and 10. The identified genomic regions may be important to improve heat tolerance in potatoes. Fine mapping of identified regions and validation of the markers associated with these regions would be required to further understand the mechanism involved in heat tolerance.