Statistical Models for Genetic Mapping in Polyploids: Challenges and Opportunities

Li, Jiahan; Das, Kiranmoy; Liu, Jingyuan; Fu, Guifang; Li, Yao; Tobias, Christian M.; Wu, Rongling

doi:10.1007/978-1-61779-785-9_13

Cited by 8 publications

(3 citation statements)

References 66 publications

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“…Statistical models for QTL mapping have been developed for polyploids with bivalent pairing, taking into account preferential vs . random chromosome pairing behavior by incorporating a preferential pairing factor [37,38]. Molecular marker segregation allows estimating chromosome pairing behavior.…”

Section: Methods For Genome Analysismentioning

confidence: 99%

Molecular Tools for Exploring Polyploid Genomes in Plants

Aversano

Ercolano²,

Caruso³

et al. 2012

IJMS

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Polyploidy is a very common phenomenon in the plant kingdom, where even diploid species are often described as paleopolyploids. The polyploid condition may bring about several advantages compared to the diploid state. Polyploids often show phenotypes that are not present in their diploid progenitors or exceed the range of the contributing species. Some of these traits may play a role in heterosis or could favor adaptation to new ecological niches. Advances in genomics and sequencing technology may create unprecedented opportunities for discovering and monitoring the molecular effects of polyploidization. Through this review, we provide an overview of technologies and strategies that may allow an in-depth analysis of polyploid genomes. After introducing some basic aspects on the origin and genetics of polyploids, we highlight the main tools available for genome and gene expression analysis and summarize major findings. In the last part of this review, the implications of next generation sequencing are briefly discussed. The accumulation of knowledge on polyploid formation, maintenance, and divergence at whole-genome and subgenome levels will not only help plant biologists to understand how plants have evolved and diversified, but also assist plant breeders in designing new strategies for crop improvement.

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Section: Methods For Genome Analysismentioning

confidence: 99%

Molecular Tools for Exploring Polyploid Genomes in Plants

Aversano

Ercolano²,

Caruso³

et al. 2012

IJMS

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“…Therefore, research into its genetics, genomics, and breeding has been limited (Habiyaremye et al, 2017b). Furthermore, genetic analysis of proso millet is also difficult because of its polyploid nature (proso is allopolyploid; 2n = 4x = 36) (Li et al, 2012). However, this crop has received more research attention lately, and availability of genomic information is increasing with access to different genomic resources.…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity and agronomic performance of Slovenian landraces of proso millet (Panicum miliaceum L.)

Flajšman¹,

Štajner²,

Ačko³

2019

Turk J Bot

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Introduction Panicum miliaceum L., most commonly named proso millet and broomcorn millet, is a member of the small millets group, which together with P. miliaceum encompasses six cereal crops: foxtail millet (Setaria italica L. Beauv), kodo millet (Paspalum scrobiculatum Michx.), finger millet (Eleusine coracana (L.) Gaertn.), little millet (Panicum sumatrense Rothex. Roem. and Schultz), and barnyard millet (Echinochloa spp.) (Goron and Raizada, 2015). According to CGIAR (Consultative Group on International Agricultural Research; http://www.cgiar.org/), proso millet has a 30% share of global millet production. Proso millet is grown for the production of small seeds, which are used as animal fodder and for human consumption (Habiyaremye et al., 2017b). P. miliaceum is a minor cereal today in terms of global economic importance, yet it is a very important food source among some of the world's poorest sections, especially for people living in hot and dry areas in developing and underdeveloped countries (Wang et al., 2016). Proso millet is one of the world's oldest cultivated cereals. It appeared as a staple crop in northern China 10,000 years ago (Lu et al., 2009), and later spread to other parts of the world, including Slovene territory where it was grown as early as 1000 BC by the Celts (Ačko, 2012). Although Slovenia is a small mid-European country (≈20 000 km 2 and ≈2 million inhabitants), proso millet was an essential dish for five centuries from the Middle Ages, when Slovene farmers consumed millet porridge on a daily basis (Ačko, 2012). Proso millet can be described by some outstanding useful characteristics. Regarding favored nutritional traits, protein content (12.5%) is the highest among all small millets, and even higher than in the major cereals, rice and wheat (Saha et al., 2016). Furthermore, proso millet is gluten-free, which makes it appropriate for gluten-intolerant people. A few reports have revealed the medicinal benefits of consuming proso millet, e.g., lowering cholesterol and phytate, inhibiting certain cancers, preventing heart and liver diseases, and managing liver dysfunctions and diabetes (Zhang et al., 2014). Proso millet also has lots of favored agronomic traits. It belongs to the grain crops which have extremely low water requirements. The reason for its drought tolerance is its short growing season, being mature within 60-90 days (Baltensperger, 1996). In addition, it can grow well in different poor soils, even with minimal agronomic input (Sabir et al., 2011). Landraces have huge economic value for local cultivation because of adaptation to the agro-Abstract: Proso millet (Panicum miliaceum L.) has many favored nutritional and agronomic traits, which makes it appropriate for cultivation and consumption all around the world. Genomic resources for proso millet are still very limited but the set of genomic data is improving. In this study, we genotyped six Slovenian landraces of proso millet (P. miliaceum L.) along with one Slovene autochthonous cultivar, Sonček. The chosen set of 11 SSR ...

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“…However, more subtle or multiple QTL are difficult to detect using GWAS ( Korte and Farlow 2013 ; Ott et al 2015 ). Similarly, improvements seen by the use of a bi-parental cross in polyploids has been limited by uncertainties around the geno-phenotype correspondence, the partially informative markers determined for this cross, variations in meiotic mechanisms, outcrossing due to heterozygous genomic structure and how allelic and nonallelic combinations increase at an exponential rate with the number of alleles and thus only QTL with a larger effect can be identified ( Li et al 2012 ).…”

mentioning

confidence: 99%

Solyntus, the New Highly Contiguous Reference Genome for Potato (Solanum tuberosum)

Lieshout

Burgt²,

Vries³

et al. 2020

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With the rapid expansion of the application of genomics and sequencing in plant breeding, there is a constant drive for better reference genomes. In potato (Solanum tuberosum), the third largest food crop in the world, the related species S. phureja, designated "DM", has been used as the most popular reference genome for the last 10 years. Here, we introduce the de novo sequenced genome of SolyntusTM as the next standard reference in potato genome studies. A true Solanum tuberosum made up of 116 contigs that is also highly homozygous, diploid, vigorous and self-compatible, SolyntusTM provides a more direct and contiguous reference then ever before available. It was constructed by sequencing with state-of-the-art long and short read technology and assembled with Canu. The 116 contigs were assembled into scaffolds to form each pseudochromosome, with three contigs to 17 contigs per chromosome. This assembly contains 93.7 % of the single-copy gene orthologs from the Solanaceae set and has an N50 of 63.7 Mbp. The genome and related files can be found at https://www.plantbreeding.wur.nl/Solyntus/. With the release of this research line and its draft genome we anticipate many exciting developments in (diploid) potato research.

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Statistical Models for Genetic Mapping in Polyploids: Challenges and Opportunities

Cited by 8 publications

References 66 publications

Molecular Tools for Exploring Polyploid Genomes in Plants

Molecular Tools for Exploring Polyploid Genomes in Plants

Genetic diversity and agronomic performance of Slovenian landraces of proso millet (Panicum miliaceum L.)

Solyntus, the New Highly Contiguous Reference Genome for Potato (Solanum tuberosum)

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