scholarly journals Sexual dimorphism and the effect of wild introgressions on recombination in Manihot esculenta

2019 ◽  
Author(s):  
Ariel W. Chan ◽  
Amy L. Williams ◽  
Jean-Luc Jannink
Keyword(s):  
Sexual Dimorphism ◽  
Genetic Map ◽  
Manihot Esculenta ◽  
Genotyping By Sequencing ◽  
Chromosome 1 ◽  
International Institute ◽  
Tropical Agriculture ◽  
Chromosome 4 ◽  
Manihot Glaziovii ◽  
Introgressed Region

ABSTRACTRecombination has essential functions in evolution, meiosis, and breeding. Here, we use the multi-generational pedigree, consisting of 7,165 informative meioses (3,679 female; 3,486 male), and genotyping-by-sequencing (GBS) data from the International Institute of Tropical Agriculture (IITA) to study recombination in cassava (Manihot esculenta). We detected recombination events using SHAPEIT2 and duoHMM, examined the recombination landscape across the 18 chromosomes of cassava and in regions with known introgressed segments from cassava’s wild relative Manihot glaziovii, constructed a genetic map and compared it to an existing map constructed by the International Cassava Genetic Map Consortium (ICGMC), and inspected patterns of recombination placement in male and female meioses to see if there is evidence of sexual dimorphism in crossover distribution and frequency. We found that the placement of crossovers along chromosomes did not vary between the two sexes but that females undergo more meiotic recombination than males. We also observed that introgressions from M. glaziovii decreased recombination in the introgressed region and, in the case of chromosome 4, along the entire length of the chromosome that the introgression is on. We observed a dosage effect on chromosome 1, possibly suggesting the presence of a variant on the M. glaziovii haplotype that leads to lower overall recombination in the introgressed region.

scholarly journals Sexual dimorphism and the effect of wild introgressions on recombination in cassava (Manihot esculenta Crantz) breeding germplasm

2021 ◽  
Author(s):  
Ariel W Chan ◽  
Seren S Villwock ◽  
Amy L Williams ◽  
Jean-Luc Jannink
Keyword(s):  
Manihot Esculenta ◽  
Genotyping By Sequencing ◽  
Genetic Maps ◽  
International Institute ◽  
Tropical Agriculture ◽  
Recombination Rates ◽  
Manihot Esculenta Crantz ◽  
Suppressed Recombination ◽  
Manihot Glaziovii ◽  
Breeding Germplasm

Abstract Recombination has essential functions in meiosis, evolution, and breeding. The frequency and distribution of crossovers dictate the generation of new allele combinations and can vary across species and between sexes. Here, we examine recombination landscapes across the 18 chromosomes of cassava (Manihot esculenta Crantz) with respect to male and female meioses and known introgressions from the wild relative Manihot glaziovii. We used SHAPEIT2 and duoHMM to infer crossovers from genotyping-by-sequencing (GBS) data and a validated multi-generational pedigree from the International Institute of Tropical Agriculture (IITA) cassava breeding germplasm consisting of 7,020 informative meioses. We then constructed new genetic maps and compared them to an existing map previously constructed by the International Cassava Genetic Map Consortium (ICGMC). We observed higher recombination rates in females compared to males, and lower recombination rates in M. glaziovii introgression segments on chromosomes 1 and 4, with suppressed recombination along the entire length of the chromosome in the case of the chromosome 4 introgression. Finally, we discuss hypothesized mechanisms underlying our observations of heterochiasmy and crossover suppression and discuss the broader implications for plant breeding.

scholarly journals Sexual dimorphism and the effect of wild introgressions on recombination in cassava (Manihot esculenta Crantz) breeding germplasm

2021 ◽  
Author(s):  
Jean-Luc Jannink ◽  
Ariel W. Chan ◽  
Seren St. Clair Villwock ◽  
Amy L Williams
Keyword(s):  
Manihot Esculenta ◽  
Genotyping By Sequencing ◽  
Genetic Maps ◽  
International Institute ◽  
Tropical Agriculture ◽  
Recombination Rates ◽  
Manihot Esculenta Crantz ◽  
Suppressed Recombination ◽  
Manihot Glaziovii ◽  
Breeding Germplasm

Recombination has essential functions in meiosis, evolution, and breeding. The frequency and distribution of crossovers dictate the generation of new allele combinations and can vary across species and between sexes. Here, we examine recombination landscapes across the 18 chromosomes of cassava (Manihot esculenta Crantz) with respect to male and female meioses and known introgressions from the wild relative Manihot glaziovii. We used SHAPEIT2 and duoHMM to infer crossovers from genotyping-by-sequencing (GBS) data and a validated multi-generational pedigree from the International Institute of Tropical Agriculture (IITA) cassava breeding germplasm consisting of 7,020 informative meioses. We then constructed new genetic maps and compared them to an existing map previously constructed by the International Cassava Genetic Map Consortium (ICGMC). We observed higher recombination rates in females compared to males, and lower recombination rates in M. glaziovii introgression segments on chromosomes 1 and 4, with suppressed recombination along the entire length of the chromosome in the case of the chromosome 4 introgression. Finally, we discuss hypothesized mechanisms underlying our observations of heterochiasmy and crossover suppression and discuss the broader implications for plant breeding.

scholarly journals DESKRIPSI KLON TANAMAN UBI KAYU (Manihot esculenta Crantz) YANG DITANAM PETANI DI ENAM KABUPATEN DI PROVINSI LAMPUNG

2021 ◽  
Vol 9 (03) ◽  
pp. 271
Author(s):  
Dany Pranowo
Keyword(s):  
Manihot Esculenta ◽  
International Institute ◽  
Tropical Agriculture ◽  
Manihot Esculenta Crantz

Penelitian ini dilakukan dengan melakukan pengumpulan data klon ubi kayu dengan melakukan survei di Way Kanan, Lampung Tengah, Lampung Utara, Pringsewu, Tanggamus, dan Metro).  Penentuan kabupaten sampel dilakukan dengan metode acak terarah berdasarkan luasan budidaya.  Pengambilan sampel desa dilakukan melalui rancangan sampling non-probablitas, yaitu sampling kebetulan (accidental sampling). Data primer diperoleh melalui wawancara kepada petani yang dijumpai di lokasi penelitian meliputi nama lokal, umur tanaman, dan penggunaan klon yang dibudidayaka.  Data deskripsi karakteristik morfologis karakteristik vegetatif didapatkan melalui pengamatan langsung di lapangan dengan standarisasi yang ditetapkan oleh International Institute of Tropical Agriculture (IITA) yaitu “Selected Morphological and Agronomic Descriptors for the Characterization of Cassava” oleh Fukuda, dkk. (2010). Ditemukan 15 klon dari 6 kabupaten/kota, di Kabupaten Lampung Tengah ditemui 3 klon ubi kayu (Barokah, Thailand, dan Kasesat), Tanggamus 2 klon (Martapuro dan Baturaja), Pringsewu 2 klon ( Melati dan Pringsewu-1), Way Kanan 3 Klon (S.R. Lowo, Way Kanan -1 dan Way Kanan-2), Kota Metro 2 klon (Manalagi dan Klenteng) dan di Lampung Utara ditemui 3 klon (Roti, Udang, dan Ketan).  Analisis klaster dilakukan untuk mengetahui struktur populasi suatu kelompok individu termasuk kemiripan (similarity) atau jarak genetik (distance) dan penyebaran kelompok tertentu dalam populasi dengan menggunakan software SPSS Statistics 23.  Terdapat 8 level, klon yang memiliki tingkat kesamaan karakter terbesar adalah klon Martapuro dan S.R Lowo.  

scholarly journals Seed Yam Production Using High-Quality Minitubers Derived from Plants Established with Vine Cuttings

Agronomy ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 978
Author(s):  
Beatrice Aighewi ◽  
Norbert Maroya ◽  
Lava Kumar ◽  
Morufat Balogun ◽  
Daniel Aihebhoria ◽  
...  
Keyword(s):  
Block Design ◽  
Research Station ◽  
International Institute ◽  
Tropical Agriculture ◽  
Single Node ◽  
Cropping Season ◽  
Randomized Complete Block Design ◽  
The World ◽  
Cropping Seasons ◽  
Set Up

Yam (Dioscorea spp.) is a valuable food security crop in West Africa, where 92% of the world production occurs. The availability of quality seed tubers for increased productivity is a major challenge. In this study, minitubers weighing 1, 3, and 5 g produced from virus-free single-node vine cuttings of two improved yam varieties (Asiedu and Kpamyo) growing in an aeroponics system were assessed for suitability in seed production at a population of 100,000 plants ha−1. A 3 × 2 factorial experiment with randomized complete block design and three replications was set up during the cropping seasons of 2017 to 2019 at the International Institute of Tropical Agriculture Research Station in Kubwa, Abuja, Nigeria. Results showed field establishments of 87%–97.8%. Yields differed with minituber size, variety, and cropping season; the highest was 31.2 t ha−1 in 2019 and the lowest, 10 t ha−1 in 2018 from 5 and 1 g Kpamyo minitubers, respectively. The estimated number of tubers produced per hectare by 1, 3, and 5 g minitubers was 101,296, 112,592, and 130,555, with mean weights per stand of 159.2, 187.3, and 249.4 g, respectively. We recommend using less than 6 g minitubers for seed yam production due to their high multiplication rates.

Genetic diversity in Bambara groundnut (Vigna subterranea L.) germplasm revealed by RAPD markers

Genome ◽  
2001 ◽  
Vol 44 (6) ◽  
pp. 995-999 ◽  
Author(s):  
H I Amadou ◽  
P J Bebeli ◽  
P J Kaltsikes
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Geographic Origin ◽  
Bambara Groundnut ◽  
International Institute ◽  
Tropical Agriculture ◽  
Vigna Subterranea ◽  
Ibadan Nigeria

Random amplified polymorphic DNA (RAPD) markers were used to assess genetic diversity in Bambara groundnut (Vigna subterranea L.) germplasm using 25 African accessions from the collection in the International Institute for Tropical Agriculture, Ibadan, Nigeria. Fifty random decamer primers were screened to assess their ability to detect polymorphism in bambara; 17 of them were selected for this study. Considerable genetic diversity was found among the V. subterranea accessions studied. The relationships among the 25 accessions were studied by cluster analysis. The dendrograms showed two main groups of accessions mainly along the lines of their geographic origin. It is concluded that RAPD can be used for germplasm classification in bambara groundnut and hence for improving this crop.Key words: germplasm, PCR, RAPD, Vigna subterranea.

scholarly journals AFLAP: Assembly-Free Linkage Analysis Pipeline using k-mers from whole genome sequencing data

2020 ◽  
Author(s):  
Kyle Fletcher ◽  
Lin Zhang ◽  
Juliana Gil ◽  
Rongkui Han ◽  
Keri Cavanaugh ◽  
...  
Keyword(s):  
Linkage Analysis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genetic Map ◽  
Genotyping By Sequencing ◽  
Genetic Maps ◽  
Whole Genome ◽  
Sequencing Data ◽  
Analysis Pipeline ◽  
Genome Assemblies

AbstractBackgroundGenetic maps are an important resource for validation of genome assemblies, trait discovery, and breeding. Next generation sequencing has enabled production of high-density genetic maps constructed with 10,000s of markers. Most current approaches require a genome assembly to identify markers. Our Assembly Free Linkage Analysis Pipeline (AFLAP) removes this requirement by using uniquely segregating k-mers as markers to rapidly construct a genotype table and perform subsequent linkage analysis. This avoids potential biases including preferential read alignment and variant calling.ResultsThe performance of AFLAP was determined in simulations and contrasted to a conventional workflow. We tested AFLAP using 100 F2 individuals of Arabidopsis thaliana, sequenced to low coverage. Genetic maps generated using k-mers contained over 130,000 markers that were concordant with the genomic assembly. The utility of AFLAP was then demonstrated by generating an accurate genetic map using genotyping-by-sequencing data of 235 recombinant inbred lines of Lactuca spp. AFLAP was then applied to 83 F1 individuals of the oomycete Bremia lactucae, sequenced to >5x coverage. The genetic map contained over 90,000 markers ordered in 19 large linkage groups. This genetic map was used to fragment, order, orient, and scaffold the genome, resulting in a much-improved reference assembly.ConclusionsAFLAP can be used to generate high density linkage maps and improve genome assemblies of any organism when a mapping population is available using whole genome sequencing or genotyping-by-sequencing data. Genetic maps produced for B. lactucae were accurately aligned to the genome and guided significant improvements of the reference assembly.

scholarly journals Effect of Soaking and Boiling on Anti-nutritional Factors, Oligosaccharide Contents and Protein Digestibility of Newly Developed Bambara Groundnut Cultivars

2017 ◽  
Vol 5 (9) ◽  
pp. 1006 ◽  
Author(s):  
Olaposi Adeleke ◽  
Oladipupo Qudus Adiamo ◽  
Olumide Samson Fawale ◽  
Gbeminiyi Olamiti
Keyword(s):  
Protein Digestibility ◽  
Bambara Groundnut ◽  
International Institute ◽  
Tropical Agriculture ◽  
Vigna Subterranea ◽  
Nutritional Factors ◽  
Nutritive Quality ◽  
Vitro Protein

Newly developed Bambara groundnut (Vigna subterranea L.) seeds (Accessions No: TVSU 5 – Bambara Groundnut White (BGW) and TVSU 146 – Bambara Groundnut Brown (BGB)) were collected from International Institute of Tropical Agriculture (IITA), Nigeria, planted and harvested. The effects of processing methods (soaking and boiling) on anti-nutritional factors and oligosaccharides content and protein digestibility of BGW and BGB compared with Bambara groundnut commercial (BGC) seeds were investigated. Soaking and boiling significantly reduced the anti-nutritional factors of the samples and the effect increased as processing time was elongated. Sample BGC had lower anti-nutritional factors than BGW and BGB after soaking for 48 h. Tannin contents of the samples were reduced drastically by 99 % throughout the soaking periods. Greatest loss in raffinose level was observed in BGB (59%) and BGW (50%) after boiling for 60 min compared with BGC (43%). The loss in stachyose content of the samples varies with processing and BGC (59%) had greatest loss after boiling for 60 min while soaking for 48 h reduced that of BGB and BGW by 57 and 35%, respectively. Boiling for 60 min increased the in vitro protein digestibility of BGB (89.34 %) compared with BGW (87.48%) and BGC (82.89%). Overall, the results demonstrated that soaking and boiling of newly developed Bambara groundnut seeds could improve the nutritive quality of the seeds.

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