Biotechnology: Impact on Sugarcane Agriculture ...

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A keynote speech at the IS-2011, November 21–25, 2011, New Delhi,. India. Y.-B. Pan ... Unit in Houma, LA in 1994 in areas such as molecular eval- uation of ...
Sugar Tech DOI 10.1007/s12355-012-0136-2

LETTER TO EDITOR

Biotechnology: Impact on Sugarcane Agriculture and Industry Yong-Bao Pan

Received: 4 January 2012 / Accepted: 10 January 2012 Ó Society for Sugar Research & Promotion 2012

The term ‘‘biotechnology’’ defined by the USDA-ARS in 1990 as ‘‘the use of living organisms, cells, sub-cellular organelles, and/or parts of those structures, as well as the molecules, to effect biological, chemical, or physical changes’’ remains true; however, how the use of these biological subjects is constantly evolving through information technology innovation and new instrument development. Today, biotechnologists are able to advance scientific knowledge in basic research in genomics, proteomics, metabolomics, etc. to understand the organization, expression, regulation, and evolution of fundamental genetic material and how these processes affect the speciation and biological function of living organisms. Biotechnologists have also had success in applied research areas such as gene cloning and sequencing, recombinant DNA, transgenic or GMO crops, biofactory, identification and utilization of molecular markers for traits, biotic and abiotic stresses, development of value added products such as bio-fuel, and marker-assisted animal and plant breeding. With the availability of a few powerful search engines (www.googlescholar.com, www.baidu.com, and www.scopus.com, etc.), researchers are able to collect most, if not all, research reports in each of the listed research areas simply by logging in and browsing the key words of interest. Life science researchers are also able to access to various DNA, RNA, and protein sequences of interest through public databases such as http://www.ncbi.nlm. nih.gov/. A keynote speech at the IS-2011, November 21–25, 2011, New Delhi, India. Y.-B. Pan (&) United States Department of Agriculture-Agricultural Research Service, Mid-South Area, Sugarcane Research Laboratory, 5883 USDA Road, Houma, LA 70360, USA e-mail: [email protected]

To those who work for the sugarcane agricultural industry, these resources are equally available. Generally speaking, there are probably nine key technology issues that affect the sustainability of sugar- or bio-energy-cane crop productivity: land, fertility, water, variety, planting density, crop protection, cultural practices, harvesting and processing, and lately, information technology. All sugarcane growers may agree that growing the right variety or varieties is perhaps the most important decision for them to ensure a profitable agricultural business. While it is the responsibility of the conventional breeders to produce good sugarcane varieties, geneticists and biotechnologists may contribute to the variety development process (crossing, selection, and evaluation) through the application of new molecular tools. Conventional sugarcane breeding is probably the most difficult job of any crop. Sugarcane cultivars (Saccharum spp. hybrids) are highly polyploidy inter-specific hybrids containing 100 to 130 chromosomes that vary across geographical areas. Other obstacles/ constraints include the small size flowers that can self pollinate and may not synchronize, the difficulty in distinguishing F1 hybrids from selfs by visual rating, the extreme genotype 9 environment effect, and potential variety mis-identification during vegetative propagation and varietal exchange, etc. It takes 12 to 14 years to develop a new sugarcane variety, which is selected and evaluated for over 20 traits that include high tonnage, high sugar yield, early maturity, low fiber, harvest ability, cold tolerance, ratooning ability, and resistance to disease and insect pests. Sr. Venkatraman, a renowned Indian sugarcane breeder, concluded at the Cane Breeding Session of 1956 ISSCT Conference that conventional sugarcane breeding was largely a hit-and-miss process and called for a ‘‘SuperSugarcane-Breeding-Station’’ with objectives extending into the fundamental and somewhat purely academic aspects of cane genetics and breeding. These topics might include sugarcane biochemistry, interspecific and intergeneric crossing,

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germplasm expedition, and breeding for production on less favorable lands. I was totally inspired by his vision to realize that the need for such a Super-Sugarcane-Breeding-Station had been even more obvious when we were marching into the twenty first century! Applied biotechnology research projects were initiated at the USDA-ARS, MSA, Sugarcane Research Unit in Houma, LA in 1994 in areas such as molecular evaluation of germplasm, species- and trait-specific (SCAR, QTL) DNA markers, molecular identity database, genetic linkage mapping, inheritance of molecular markers, and transgenic (GMO) sugarcane. Anyone who is interested in the output of these biotechnology research projects may access the website: http://www.ars.usda.gov/main/site_main.htm?modecode=6410-00-00. In this presentation, I will focus on the utility of a newly developed sugarcane molecular identity database based on polymorphic microsatellite (SSR) DNA markers developed by the International Consortium of Sugarcane Biotechnologists (ICSB) founded by James Irvine. Unlike morphological traits that may vary due to G 9 E interactions, SSR DNA markers-based molecular identities that are defined by the presence or absence of 144 distinctive alleles from 21 ICSB SSR markers in a sequential order, are stable. The molecular identity of any sugarcane clone is unique and remains the same regardless of when or where the cane is grown. The quality and reliability of sugarcane molecular identities are ensured by a high throughput SSR genotyping technology that utilizes leaf tissue DNA samples, a liquidhandling station, 384-well reaction plates, fluorescencelabeled PCR primers, and capillary electrophoresis

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(CE)-based DNA sequencers. Robust, yet distinctive, fluorescence peaks or SSR alleles are revealed from the CE files with GeneMapper software and sizes of these SSR alleles from each sample are accurately determined by calibration against 15 fluorescence-labeled size standards in the range of 35 to 500 bp. Since 2005, molecular identities have been constructed for over 1,500 clones of sugarcane cultivars and related Saccharum species (S. officinarum, S. spontaneum, S. robustum, S. barberi, S. sinense, and S. edule). Geographical areas included Argentina, Australia, Bangladesh, China, Colombia, India, Mexico, Pakistan, South Africa, Thailand, U.S. (Louisiana, Florida, Texas, and Hawaii), and Venezuela. These molecular identities have been successfully utilized to promote the efficiency of the USDA-ARS, SRL’s conventional sugarcane breeding program in the following areas by: (1) Providing molecular descriptors to recent variety registration articles; (2) Identifying and removal of mis-labeled clones from crossing carts; (3) Developing de novo clones of energy cane with S. spontaneum cytoplasm; (4) Determining paternity of progeny of polycrosses; (5) Determining genetic relatedness of parental clones; (6) Assessing cross fidelity, defined as the proportion of progeny that inherit SSR alleles from both parents, to highlight the role of pollen control during crossing; and (7) Identifying F1 hybrids from (elite 9 wild) or (wild 9 elite) crosses. In addition, the availability of these molecular identities has also facilitated genetic studies on the inheritance mechanism of SSR markers in sugarcane.