Unraveling the genome sequence information reveals molecular process of tuberization and disease resistance in potato (Solanum tuberosum L.)
Authors: Dipul K Biswas, Rohini Sreevathsa, Rhitu Rai, Prasanta K Dash
ICAR-National Research Centre on Plant Biotechnology, LBS Building, PUSA, New Delhi-110012.
Potato (Solanum tuberosum L.) is the fourth most important food crop consumed in the world, following wheat, rice, and maize. It is also world's most popular vegetable, and is used in multiple cuisines of countries around the globe. In India it is used in curries in India and in pasta in Italy, stewed with bananas in Costa Rica, and is stir-fried with other green vegetables in many countries. While the choice of tubers limits its culinary applications, modern varieties of potato offer a wide range of cooking choices suitable for hundreds of different dishes. Some potato varieties are important ingredients of soups while other varieties are baked or served as simple snack.
Nutritionally, potato contains vitamins and minerals, as well as an assortment of phytochemicals, such as carotenoids and natural phenols. It is one of the most common food sources to contain multiple health benefit elements that make it a world-wide staple dietary food. The health benefits include their ability to improve digestion, reduce cholesterol, boost heart health, and strengthen the immune system. A medium-size potato contains high levels of potassium and provides nearly half the daily adult requirement of vitamin C. Besides, it is also a good source of B vitamins, and minerals such as phosphorus and magnesium.
Potato origin and agronomy
Potato is believed to have originated in the mountainous west-central region of the South American continent and speculated to have been first cultivated in South America between three to seven thousand years ago. However, in the absence of direct proof of its cultivation, it is believed that it might have been grown in that region 13,000 years ago. The native Indians in Peru were believed to be the first cultivators of potato around 8,000 BC to 5,000 B.C. It was used as a stable, high-calorie food during crop failure and famine in Europe in late 1700s. Later, it was grown in a variety of European climates producing high yield and used for livestock as well as human consumption. Ireland became particularly dependent on potato cultivation by the mid-1800s. Historically, after three consecutive failures of potato crop (1845-1848) due to late-blight disease, more than 1.5 million people perished or emigrated out of Ireland.
Potato as a crop is highly adaptable to a wide variety of farming systems. It is grown in more than 100 countries under temperate, subtropical and tropical conditions and is a "cool weather crop". According to FAO statistics, potato production in developing countries has increased by 94.6 percent over the last 15 years. Especially in the developing countries, its importance has grown rapidly with production reaching 364 million tons (http://www.fao.org). Temperature fluctuation during its growth and tuberization is a cardinal limiting factor of potato production as growth of tubers is reduced in temperature less than 10°C and more than 30°C. The optimum temperature for higher yield in this cool weather crop is between 18°C-20°C. For that reason, potato is planted in early spring in temperate zones and in late-winter in warmer regions, and grown during the coolest months of the year in hot tropical climates. As per global production, India ranks third in potato production behind China and Russia.
Potato propagation and taxonomy
Taxonomically, potato belongs to solanaceae family which includes other members such as tomato, eggplant and bell-pepper. Worldwide more than 4,000 varieties of potato are seen that come in many sizes and shapes. The potatoes grow under soil are the swollen portion of the underground stem that are called tubers (Hijmans RJ. 2001). The stem tubers, latter enlarge/thicken to develop into storage organs (Burlingame et al. 2009). The tuber has all the parts of a normal stem, including nodes and internodes. The above ground plants are herbaceous perennials (60cm in height) but the leaves die back after tuber formation. Potato is vegetatively propagated, meaning a new plant can be grown from a potato or piece of potato, called a "seed". The new plant can produce 5-20 new tubers, which are genetic clones of the mother seed plant (Fernie and Willmitzer. 2009). Potato has a variety of uniqueness besides its clonal propagation. When left in field, the tuber is produced in one growing season and perennates the plant as a means of propagation. At the onset of winter, the above-ground parts such as leaf/stem of the plant dies but the tubers over-winter underground until spring season. When a favorable time comes, they regenerate new shoots that uses the stored food of the tuber to grow. As the main shoot develops adventitious roots from base of the stem and lateral buds ramify on the shoot and the stolon elongates during long days. While root growth of the stolon is prevented by high auxin level, lipoxygenase enzymes make endogenous hormones during tuber development.
Genome and genomics of potato
Recently, genomes of several crop species have been decoded (Wang et al., 2012) and the genomic information (Dash et al., 2014) is being used for understanding specific molecular processes inherent to that crop (Dash et al., 2016; Yadav et al., 2016) .The potato genome consists of 12 chromosomes and the genome size is approximately 840 Mbp (Armuganathan and Earle., 1991). Cultivated potato varieties are autotetraploid (2n = 4x = 48) and are highly heterozygous. Owing to the polyploidy nature, its genome sequence and assembly was a complicated process. However, the genome sequence was decoded by the International Potato Genome Sequencing Consortium (PGSC) in 2011. To get rid of genetic heterozygosity and generate a high-quality draft genome sequence, the consortia used two different genotypes of potato for sequencing. One represented a homozygous doubled monoploid S. tuberosum Phureja DM1-3 which was derived by tissue culture techniques (Paz and Veilleux., 1999) while the second one was heterozygous diploid S. tuberosum group tuberosum RH89-039-16. The two different genotypes used for sequencing represent potato genom diversity i.e (1) DM (Phureja DM1-3 ) with its fingerling (elongated) tubers a derivative of primitive South American cultivar whereas (2) RH (tuberosum RH89-039-16) closely resembles commercially cultivated tetraploid potato (Fig 1). A hybrid approach of sequencing that involved Illumina, Roche and standard Sanger's DNA sequencing method was adopted for genome decoding and sequences of both were merged to arrive at a consensus genome data. The deduced genome assembly was of 726 Mbp and represented 86% of the predicted genome of 840 Mbp. It is predicted there are 39,031 genes in potato genome. The genome sequence also revealed presence of 62.2% repetitive sequences that have long terminal repeat retro-transposons. In addition, sub-telomeric repeats were identified to end of the chromosomes.
Tuberization in potato
Comparison of tuber development between the contrasting DM and RH genotypes revealed 15,235 genes were involved in the transition from stolons to tubers. Specifically, 1,217 transcripts exhibited five-fold difference in expression between stolon and tuber tissues. Among the upregulated genes, 333 transcripts were up-regulated during transition from stolon to tuber (Prat et al., 1990). Notable among them code for storage proteins (Shewry PR. 2003) such as proteinase inhibitors and patatin (15 genes). It was observed that stolon to tuber transition also coincides with 3-8-fold up-regulation of starch biosynthesis in plastids. Also there is a difference in hydrolytic and phosphorolytic starch degradation enzymes in tubers. Higher amount of amylase activity was observed in stolon producing DM variety compared to tuber producing RH variety. It is speculated that, differences of gene expression between the breeding line RH and the primitive DM will lead to identification of some candidate genes that can be modulated to increase tuber yield.
Disease resistance genes in potato
High heterozygosity and inbreeding depression are inherent to potato because it is predominantly an out-crossing plant but propagated by vegetative method. Thus, it is susceptible to many diseases that affect all parts of the plant and cause severe reduction both in tuber quality and yield. One of the important diseases was late-blight of potato that caused Irish famine and devastated the livelihood of people of Ireland. Even today potato is affected by dreaded late-blight disease (Ronning et al., 2003) caused by Phytophthora infestans, considered the most important potato pathogen and crop is destroyed within one week in pathogen-conducive climatic conditions. Genome sequencing revealed presence of many disease resistance genes in potato. All the resistance genes are typical R genes encoding two domains such as (i) Nucleotide-binding site (NBS) domain and (ii) leucine-rich-repeat (LRR) domains. The genome of DM cultivar also contained 408 NBS-LRR-encoding genes in addition to already cloned and characterized R1, RB, R2 etc. late-blight resistance genes of potato.
Potato breeding and varietal improvement has been a difficult task to be accomplished by plant breeders as the crop is polyploidy and many important qualitative and quantitative agronomic traits are poorly understood. Thus, an understanding of its genetic composition was an essential requirement for developing more efficient breeding methods. Given the pivotal role of potato in global food security, its genome sequence provides genomic insight to be used by plant breeders for potato improvement.
Figure 1: Potato varieties DM and RH used for genome sequencing and their plant and tuber phenotypes. (Figure Source: Nature. 2011 Jul 10; 475 (7355):189-95.doi:10.1038/nature10158. Permission number: 3925890347223, Permission date: Aug 11, 2016).
1. Arumuganathan, K. & Earle, E. Nuclear DNA content of some important plant species. Plant Mol. Biol. Rep. 9, 208-218 (1991).
2. Burlingame, B., Mouille , B. & Charrondie re, R. Nutrients, bioactive non-nutrients and anti-nutrients in potatoes. J. Food Compost. Anal. 22, 494-502 (2009).
3. Dash PK et al. (2014). Genome-wide analysis of drought induced gene expression changes in Linum usitatissimum. GM Crops Food. 5(2):106-19.
4. Dash, PK et al. (2016). Carrot Genome Provides Insights into Root Accumulation of Carotenoid. Biotecharticles.
5. Fernie AR, Willmitzer L. Molecular and biochemical triggers of potato tuber development. Plant Physiol. 2001 Dec; 127(4):1459-65.
6. Hijmans, R. J. Global distribution of the potato crop. Am. J.Potato Res. 78, 403-412 (2001).
7. Paz, M. M. & Veilleux, R. E. Influence of culture medium and in vitro conditions on shoot regeneration in Solanum phureja monoploids and fertility of regenerated doubled monoploids. Plant Breed. 118, 53-57 (1999).
8. Prat, S. et al. Gene expression during tuber development in potato plants. FEBS Lett. 268, 334-338 (1990).
9. Ronning CM et al. Comparative analyses of potato expressed sequence tag libraries. Plant Physiol. 2003 Feb; 131(2):419-29.
10. Shewry PR. Tuber storage proteins. Ann Bot. 2003 Jun; 91(7):755-69.
11. The potato genome sequence consortium. (2011). Genome sequence and analysis of the tuber crop potato. Nature. 475: 189-195.
12. Wang Z et al. (2012). The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads. The Plant J. 72(3):461-473.
13. Yadav, AK et al. (2016). Genomic approaches to impart extended shelf-life in tomato. Biotech articles.
About Author / Additional Info:
Senior Scientist, Plant Biotechnology.