Borlaug legacy

Nobel Laureate Norman E. Borlaug certainly took advantage of plant genetic resources as he bred new varieties of wheat that are said to have saved the lives of perhaps one billion people via the Green Revolution (Vietmeyer, Reference Vietmeyer2008, Reference Vietmeyer2009, Reference Vietmeyer2010, Reference Vietmeyer2011). He used sources of stem rust resistance to stave off that devastating disease. His use of what became known as Shuttle Breeding using two breeding sites and selecting for superior yielding lines in each led to the development of photoperiod-insensitive lines that would give outstanding yields in a variety of environments such as Mexico, India and Pakistan. In addition, he utilized plant genetic resources that had genes to shorten and strengthen the wheat straw so that enhanced agronomic practices such as irrigation and fertilization would manifest in phenomenal increases in yield. This clearly illustrates that plant genetic resources are important for food security.

World population

World population has soared in recent human history. The current rate of growth is about one billion people added to this planet every 14 years. Ambassador Kenneth Quinn, President of the World Food Prize Foundation, said that ‘The last 50–60 years has been the single greatest period of food production and hunger reduction in all human history’ (pers. commun.). So, the question is whether we can sustain that history as we approach nine billion people by 2050.

Value of genetic resources

What is the value of genetic variation in crop breeding? Most studies reveal that 50% of the increase in crop productivity is due to genetic improvement. Genetic resources have played important roles – such as semi-dwarf wheat and rice. Agricultural productivity depends on genetic variation, and arguably, any additional knowledge of genetic variation is important in crop improvement. L. J. Stadler ushered in the era of induced mutations in plants 85 years ago (1928). The year 2013 is the 60-year anniversary since Watson and Crick (Reference Watson and Crick1953) have published on the structure of DNA and its mode of replication. Devos and Gale (Reference Devos and Gale2000) presented the comparative genomics of many grasses depicted by genome circles illustrating that information obtained for one species can be used to predict genes and gene locations in related species. These events and subsequent genomic techniques allow for the recognition and selection of useful genetic variation.

Applications

Early and continuing uses of genomics involve the employment of molecular markers to check purity, degree of inbreeding, and proof of patent infringement and many other applications. Additional exciting examples of the application of genomics now abound: (1) The International Rice Research Institute (IRRI) has bred at least ten megavarieties with the submergence-1 gene using marker-assisted selection that allowed sub-1 varieties to be developed in 2.5 years (Neeraja et al., Reference Neeraja, Maghirang-Rodriguez, Pamplona, Heuer, Collard, Septiningsih, Vergara, Sanchez, Xu, Ismail and Mackill2007). At least 100,000 farmers are now growing these varieties in flood-prone areas. (2) Pro-Vitamin A Golden Rice with the yellow carotenoid trait from maize is another exciting example in that it could save 500,000 children per year from going blind due to vitamin A deficiency (Potrykus, Reference Potrykus2001). (3) Bt corn in the Philippines provides 40–60% higher yields than conventional varieties. Although the seed costs more, it still increases net income by about 34%. Food and feed are safer due to minimizing insect damage and lowering levels of harmful human carcinogens (Panopio and Mercado, Reference Panopio and Mercado2011).

Genetic variation

We are learning that greater genetic diversity exists than ever before expected; for example, inbred lines of corn vary more from each other than humans differ from chimpanzees. Even more unexpected was the finding that many genes known in various lines are not present in the maize reference genome (B73). RNAseq on 500 inbreds revealed 8681 assembled transcripts that were not in the reference (Hansey et al., Reference Hansey, Vaillancourt, Sekhon, de Leon, Kaeppler and Buell2012). The current concept is that there is a ‘pan genome’ comprising a ‘core genome’ and a ‘dispensable genome’. One can ask: ‘Are we selecting based on the dispensable genome? Does compensation by the dispensable genomes of two parents affect heterosis?’

Questions arising

Genomic information raises many other questions. We now know that copy number variation (CNV) is common in crop genomes. Is the variation in some traits due to CNV? Soybean cyst nematode resistance appears to be due to ten copies of a sequence that increases the expression of a repeated multigene segment (Cook et al., Reference Cook, Lee, Guo, Melito, Wang, Bayless, Wang, Hughes, Willis, Clemente, Diers, Jiang, Hudson and Bent2012). Having mutations in a variety of genes has always provided an important toolbox for genetic analysis. Today, there is an interest in having available a mutant for every gene; it is estimated that between 180,000 and 460,000 would be the number of mutant lines required in rice. There are currently about 200,000 mutant lines available for rice. Directed mutations are possible via zinc finger nucleases and Transcription Activator-Like Effector Nucleases and now by Clustered Regularly Interspaced Short Palindromic Repeats (Pennisi, Reference Pennisi2013).

The first 50 plant genomes

DNA sequence data for more than 50 plant genomes have been published (Michael and Jackson, Reference Michael and Jackson2013). Even though 73% of these genomes are of crop species, still more data are necessary to assess the range of genetic resources that are available. Even partial genome assembly provides the basis for incorporating genomic information in breeding schemes.

Sequencing reference genomes and resequencing

The cost of sequencing a megabase of DNA is about $0.10 today. In 2001, the cost was $10,000. This allows extensive resequencing comparing against the reference genome. Phillips (Reference Phillips2009) proposed to ‘sequence the entire rice germplasm collection of 100,000 accessions in the IRRI gene bank’. Since then, the IRRI and the Beijing Genome Institute (BGI) have sequenced 3000 rice lines. McCouch et al. (Reference McCouch, McNally, Wang and Sackville Hamilton2012) discussed the role of genomics in assessing gene bank materials.

The relatively low cost of sequencing has led to the sequencing of multiple accessions of species. Varshney et al. (Reference Varshney, Song, Saxena, Azam, Yu, Sharpe, Cannon, Baek, Rosen, Tar'an, Millan, Zhang, Ramsay, Iwata, Wang, Nelson, Farmer, Gaur, Soderlund, Penmetsa, Xu, Bharti, He, Winter, Zhao, Hane, Carrasquilla-Garcia, Condie, Upadhyaya, Luo, Thudi, Gowda, Singh, Lichtenzveig, Gali, Rubio, Nadarajan, Dolezel, Bansal, Xu, Edwards, Zhang, Kahl, Gil, Singh, Datta, Jackson, Wang and Cook2013) sequenced the CDC Frontier variety of chickpea and resequenced 90 cultivated and wild genotypes. About 450 Oryza rufipogon accessions have been sequenced from different geographical regions (Huang et al., Reference Huang, Kurata, Wei, Wang, Wang, Zhao, Zhao, Liu, Lu, Li, Guo, Lu, Zhou, Fan, Weng, Zhu, Huang, Zhang, Wang, Feng, Furuumi, Kubo, Miyabayashi, Yuan, Xu, Dong, Zhan, Li, Fujiyama, Toyoda, Lu, Feng, Qian, Li and Han2012).

Molecular genetic markers

Single-nucleotide polymorphisms (SNPs) have been found to be extremely numerous. Based on 20 diverse varieties and landraces, McNally et al. (Reference McNally, Childs, Bohnert, Davidson, Zhao, Ulat, Zeller, Clark, Hoen, Bureau, Stokowski, Ballinger, Frazer, Cox, Padhukasahasram, Bustamante, Weigel, Mackill, Bruskiewich, Rätsch, Buell, Leung and Leach2009) reported 160,000 SNPs for rice. In chickpea, 76,000 SNPs were followed by Gaur et al. (Reference Gaur, Azam, Jeena, Khan, Choudhary, Jain, Yadav, Tyagi, Chattopadhyay and Bhatia2012). SNPs do not reveal all the variation. There are indels, inversions, translocations and CNVs. Transposable elements allow forward and reverse genetics; some estimates indicate that there are perhaps a million tagged sites available in japonica rice.

Variation not present in the parents sometimes occurs in the progeny – termed de novo variation. Such variation can be from intragenic recombination, unequal crossing over, naturally occurring point mutations, transposable elements, DNA methylation, paramutation and gene amplification (Rasmusson and Phillips, Reference Rasmusson and Phillips1997).

Wide hybridization followed by uniparental chromosome loss (Phillips and Rines, Reference Phillips, Rines, Bennetzen and Hake2009) leads to the introgression of whole chromosomes or partial chromosomes (via irradiation of the addition lines). Every chromosome of maize has been introduced into oat by this approach. As oats is a C3 species and maize is a C4 species, the introduction of C4 characteristics into oat might be possible by this procedure (Kowles et al., Reference Kowles, Walch, Minnerath, Bernacchi, Stec, Rines and Phillips2008; Tolley et al., Reference Tolley, Sage, Langsdale and Hibberd2012).

Biotech crops

Individual genes or cassettes of genes can now be added to recipient varieties by genetic engineering (James, Reference James2011). Biotech crops in which one or more important traits have been introduced via genetic engineering are now being grown on 700 million acres by seven million farmers. The acreage of biotech crops grown in developing countries has now surpassed that of crops grown in developed countries. This technology widens the range of available genetic resources.