![\"60](\"http:\/\/www.generationcp.org\/sunsetblog\/wp-content\/uploads\/2014\/12\/acid-soil-map-and-key_w1.jpg\" "\\"Credit:")
<\/a>Acidity prevents crops from accessing the right balance of nutrients in the soil, limiting farmers\u2019 yields. Its negative effect on world yield is second only to drought and is particularly hard felt by subsistent and smallholder farmers who cannot afford to correct soil pH using calcium-rich lime. As a result, these farmers are forced to grow less profitable, acid-tolerant crops like millet, or suffer huge yield losses when growing more popular cereal crops like wheat, rice or maize.<\/p>\n
\u201cIn Kenya, acidic soils cover almost 90 percent of the maize-growing areas and can reduce yields by almost 60 percent,\u201d says Samuel Gudu, Professor and Deputy Vice-Chancellor (Planning & Development) at Moi University in Kenya. \u201cFarmers know that the soil affects their yields, but they still grow maize because it is so popular.\u201d<\/p>\n
As is true in many other sub-Saharan countries, maize is a staple of the Kenyan diet: the average Kenyan consumes 98 kilograms of it each year. But maize prices in Kenya are among the highest in Africa, which directly affects the poorest quarter of the population, who spend 28 percent of their income on the crop.<\/p>\n
\u201cYield losses play a big part in this economic imbalance and are why we need affordable agronomic options to help our farmers improve yields,\u201d says Samuel, who was a Principal Investigator of a GCP comparative genomics project which sought to provide some of these options.<\/p>\n Between 2004 and 2014, crop researchers and plant breeders across five continents collaborated on several GCP projects to develop local varieties of maize, rice and sorghum that can withstand phosphorus deficiency and aluminium toxicity \u2013 two of the most widespread constraints leading to poor crop productivity in acidic soils.<\/p>\n Aluminium toxicity is the primary limitation on crop production for more than 30 percent of farmland in Southeast Asia and Latin America and approximately 20 percent in East Asia, sub-Saharan Africa and North America. Aluminium becomes more soluble in acid souls, creating a toxic glut of aluminium ions that damage roots and impair their growth and function. This results in reduced nutrient and water uptake, which in turn depresses yield.<\/p>\n Phosphorus deficiency is the next biggest soil deficiency after nitrogen to limit plant production. In acid soils, phosphorus is stuck (fixed) in forms that plants cannot take up. All plants need phosphorus to survive and thrive; it is a key element in plant metabolism, root growth, maturity and yield. Plants deficient in phosphorus are often stunted.<\/p>\n In a double whammy, the damage that aluminium toxicity causes to roots means that plants cannot efficiently access native soil phosphorus or even added phosphorus fertiliser \u2013 and adding phosphorus is an option that is rapidly becoming less viable.<\/p>\n \u201cThe world is running out of phosphorus as quickly as it is running out of oil,\u201d says Leon Kochian, a Professor in the Departments of Plant Biology and Crop and Soil Science at Cornell University in the USA. \u201cThis is making its application a more expensive and less sustainable option for all farmers wanting to improve yields on acidic soils.\u201d Indeed, the price of rock phosphate has more than doubled since 2007.<\/p>\n For 30 years, Leon has combined lecturing and supervising duties at Cornell University and the United States Department of Agriculture with his scientific quest to understand the genetic and physiological mechanisms that allow some cereals to tolerate acidic soils while others wither. And for the last 10 years, he has played an important leading role in GCP\u2019s effort to develop new, higher yielding varieties of maize, rice and sorghum that tolerate acidic soils.<\/p>\n The rationale behind GCP\u2019s efforts stems from two independent and concurrent projects, which had been flourishing on different sides of the Pacific well before GCP was created.<\/p>\n One of those projects was co-led by Leon at Cornell University in collaboration with a previous PhD student of his, Jurandir Magalh\u00e3es, at the Brazilian Corporation of Agricultural Research (EMBRAPA) Maize & Sorghum research centre.<\/p>\n Working on the understanding that the cells in grasses like barley and wheat use \u2018membrane transporters\u2019 to insulate themselves against excessive subsoil aluminium, Leon and Jurandir searched for a similar transporter in the cells of sorghum varieties that were known to tolerate aluminium.<\/p>\n \u201cIn wheat, when aluminium levels are high, these membrane transporters prompt organic acid release from the tip of the root,\u201d explains Jurandir. \u201cThe organic acid binds with the aluminium ion, preventing it from entering the root.\u201d Jurandir\u2019s team found that in certain sorghum varieties, the gene SbMATE<\/em> encodes a specialised organic acid transport protein, which stimulates the release of citric acid. They cloned the gene and found it was very active in aluminium-tolerant sorghum varieties. They also discovered that the activity of SbMATE<\/em> increases the longer the plant is exposed to high levels of aluminium.<\/p>\n The other project, co-led by Matthias Wissuwa at Japan International Research Centre for Agricultural Sciences (JIRCAS) and Sigrid Heur at the International Rice Research Institute (IRRI) in The Philippines, was looking for genes that could improve rice yields in phosphorus-deficient soils. They had already identified a gene locus (a section of the genome containing a collection of genes) that produced a protein which allowed rice varieties with to grow successfully in low-phosphorous conditions. The locus was termed \u2018phosphorus uptake 1\u2019 or Pup1<\/em> for short. With GCP support, the team were able to make the breakthrough of discovering the protein kinase gene responsible, PSTOL1 <\/em>(\u2018phosphorus starvation tolerance 1\u2019), and understanding its mechanism.<\/p>\n \u201cIn phosphorus-poor soils, this protein instructs the plant to grow larger, longer roots, which are able to forage through more soil to absorb and store more nutrients,\u201d explains Sigrid, a plant geneticist at IRRI and a GCP Principal Investigator. \u201cBy having a larger root surface area, plants can explore a greater area in the soil and find more phosphorus than usual. It\u2019s like having a larger sponge to absorb more water.\u201d<\/p>\n Leon clarifies that both projects were fairly advanced before they became part of the GCP fold. \u201cOur team had already identified the gene SbMATE<\/em> and were in the process of cloning it for breeding purposes. The IRRI and JIRCAS team had also identified Pup1<\/em> and were in the process of identifying and cloning the gene.\u201d<\/p>\n The purpose of cloning these genes was to create molecular markers to help breeders identify whether the genes were present in the varieties they were working with. As an analogy, think of \u2018reading\u2019 a plant\u2019s genome as you would read a story: the story\u2019s words are the plant\u2019s genes, and a molecular marker works as a text highlighter. Different markers can highlight or tag different keywords in the story. Tagging the location of beneficial genes in the DNA of plant genomes allows scientists to see which of the plants or seeds they are interested in \u2013 perhaps only a few out of hundreds or thousands \u2013 contain these genes. This forms the basis of marker-assisted breeding, which can help plant breeders halve the time it takes them to breed new high-yielding varieties for acidic soil conditions.<\/p>\n Leon says that GCP provided both projects with the opportunity to validate their discoveries and to use what they had found to develop new aluminium-tolerant sorghum varieties and phosphorus-efficient rice varieties for farmers. But it\u2019s what happened next that made this GCP initiative unique.<\/p>\n Sorghum, rice, maize and wheat are all part of the Poaceae (true grasses) family, evolving from a common grass ancestor 65 million years ago. Over this time, they have become very different from each other. However, at the genetic level they still have a lot in common.<\/p>\n Over the last 20 years, genetic researchers all over the world have been mapping these cereals\u2019 genomes. These maps are now being used by geneticists and plant breeders to identify similarities and differences between the genes of different cereal species. This process is termed \u2018comparative genomics\u2019 and was a fundamental research theme for GCP during its second phase (2008\u20132014).<\/p>\n \u201cThe objective during GCP Phase I (2004-2007) was to study the genomes of important crops and identify genes conferring resistance or tolerance to various stresses, such as drought,\u201d says Rajeev Varshney, Director of the Center of Excellence in Genomics at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT). \u201cThis research was long and intensive, but it set a firm foundation for the work in GCP\u2019s second phase, which sought to use what we have learnt in the laboratory and apply it to breed better varieties of crops.\u201d<\/p>\n Rajeev oversaw GCP\u2019s comparative genomics research projects on aluminium tolerance and phosphorus deficiency in sorghum, maize and rice, as part of his GCP role as Leader of the Comparative and Applied Genomics Research Theme.<\/p>\n \u201cThe idea behind the sorghum, maize and rice initiative was to use the discoveries we had independently made in sorghum and rice to see if we could find the same genes in the other crop,\u201d explains Rajeev. \u201cIn other words, we wanted to see if we could find PSTOL1<\/em> in sorghum and SbMATE<\/em> in rice.\u201d<\/p>\n Working together through a number of comparative genomics projects, the researchers were highly successful in reaching this goal, discovering valuable sister genes and beginning to introduce them into new improved crop varieties for farmers.<\/p>\n Researchers at Cornell and EMBRAPA had already been using similar comparative techniques to look for SbMATE<\/em> in maize because of its close familial connection to sorghum. This research was overseen by Leon and another EMBRAPA researcher, Claudia Guimar\u00e3es.<\/p>\n \u201cWe used the knowledge that Jurandir and Leon\u2019s SbMATE<\/em> project produced to prove that we had a major aluminium-tolerance gene,\u201d reflects Claudia.<\/p>\n The SbMATE<\/em> gene in sorghum explains about 80 percent of its aluminium tolerance, but Claudia says that in maize it explains only about 20 per cent, making it harder for researchers to find without a little help knowing what to look for. \u201cSo we had to dig a little deeper for other similar genes that confer aluminium tolerance, and we found ZmMATE<\/em>.\u201d<\/p>\n ZmMATE1<\/em> has a similar genetic sequence to SbMATE<\/em> and encodes a similar protein membrane transporter that releases citric acid from the roots. Just as in sorghum, citric acid binds to aluminium in the soil, making it difficult for it to enter plant roots. The team have also discovered related gene ZmMATE2<\/em>, which also encodes a transporter protein, but appears to confer aluminium tolerance via a different mechanism, as yet unclear.<\/p>\n Claudia has developed a number of molecular markers for ZmMATE<\/em>, which have been successfully used by breeders at EMBRAPA as well as by African partners in Niger and Kenya, such as Samuel Gudu, to identify maize breeding lines that have the gene.<\/p>\n \u201cWe used aluminium-tolerant maize varieties sourced locally and from Brazil to develop a range of potential new varieties,\u201d says Samuel. \u201cThe goal is to develop varieties that are suited to our environment and not too dissimilar to varieties that Kenyan farmers like to grow, except they have a higher tolerance to aluminium toxicity.\u201d<\/p>\n Involving farmers in the crop breeding process is an important part of such programs being successful, explains Samuel. \u201cThey help us identify maize varieties that they have observed have higher tolerance to acidic soils. We also try to incorporate other features that they want, such as disease resistance and higher yield. By incorporating their feedback into the breeding process they are more likely to grow any new varieties, as they have played a part in their development.\u201d<\/p>\n Samuel says they have developed some local aluminium-tolerant varieties, which rank among the best for aluminium tolerance. Interestingly, these varieties seem to have a different aluminium-tolerance mechanism to the Brazilian varieties.<\/p>\n \u201cFrom the work Samuel has done, we\u2019ve possibly identified a novel source of aluminium tolerance in Kenyan maize varieties,\u201d says Claudia. \u201cWe are now working together with Leon to identify the genes that are conferring this tolerance so we can develop markers to help Kenyan maize breeders also identify these varieties more efficiently.\u201d<\/p>\n To help in the process, Samuel and his team are developing single-cross hybrids with a combination of both the novel Kenyan sources of aluminium tolerance and ZmMATE<\/em> from Brazil, which will be even more tolerant to acidic soils.<\/p>\n In Asia, about 60 percent of rainfed rice is grown on soils that are affected by multiple stresses. These typically include phosphorus deficiency as well as aluminium toxicity, salinity and drought.<\/p>\n These stresses are particularly hard felt in Indonesia, which is the world\u2019s third-largest rice producer. Joko Prasetiyono is a molecular rice breeder at the Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development (ICABIOGRAD). His team have been collaborating with IRRI and JIRCAS for many years and contributed to validating the effect of Pup1<\/em> by embedding it into three popular local rice varieties \u2013 Dodokan<\/em>, Situ Bagendit<\/em> and Batur<\/em> \u2013 which were then able to tolerate phosphorus-deficient conditions.<\/p>\n \u201cThe aim [with GCP research] was to breed varieties identical to those that farmers already know and trust, except that they have PSTOL1<\/em> and an improved ability to take up soil phosphorus,\u201d says Joko.<\/p>\n Joko says that these varieties \u2013 which will be available in one to two years \u2013 will yield as well as, if not better than, traditional varieties, and will need 30\u201350 percent less fertiliser.<\/p>\n But the work is only partly finished for Joko and his Asian partners. They are now building on previous work done at Cornell and EMBRAPA to include the SbMATE<\/em> gene in their varieties. \u201cHigher yields will only be possible if the plant can also tolerate excess aluminium, which severely inhibits root growth and thereby water and nutrient uptake,\u201d explains Joko. \u201cWe are also looking at incorporating salt-tolerance and drought-tolerance genes. It\u2019s a step-by-step process where we hope to build tolerance to the multiple stresses that afflict most rice-growing areas throughout Asia and the world.\u201d<\/p>\n At EMBRAPA, Claudia is also interested in building up tolerance to multiple stresses and was involved in the project to look for genes similar to PSTOL1<\/em> in maize. \u201cAs soon as IRRI and JIRCAS had cloned the gene and created markers, we started using the markers to search for the gene in maize, as Jurandir did in sorghum,\u201d she says.<\/p>\n Finding genes that confer phosphorus-efficiency traits in maize and sorghum has been a more challenging project, according to Leon. \u201cFrom the rice work, we knew a big part of phosphorus efficiency was to do with root architecture \u2013 you want to have shallow horizontal roots instead of roots that grow down, which is often the case in maize and sorghum,\u201d he explains. \u201cThis is because there is less accessible phosphorus further down the soil profile.\u201d<\/p>\n Observing root architecture is difficult in ordinary soil, so the team had to develop new ways to visualise the plants\u2019 roots. They grew plants in a transparent nutrient gel, which they then photographed to create three-dimensional images of the root structure.<\/p>\n The team found sorghum and maize varieties that contained genes similar to PSTOL1<\/em> in rice, but which also have longer root systems that radiated outwards rather than downwards in gels with higher concentration of aluminium. \u201cThese observations helped validate multiple PSTOL1 <\/em>regions in sorghum and maize, which we\u2019ve been able to develop markers for to help breeders identify these traits more easily,\u201d says Leon.<\/p>\n These markers have successfully been used by sorghum breeders in Brazil and Africa to identify phosphorus-efficient varieties. Maize breeders in both Brazil and Africa are expected to use similar markers to validate their varieties in 2015.<\/p>\n Eva Weltzien is one Africa-based sorghum breeder who has benefited from these PSTOL1<\/em> and SbMATE<\/em> markers. Based in Mali at ICRISAT, Eva and her team have been using the markers to select for aluminium-tolerant and phosphorus-efficient varieties and validating their performance in field trials across 29 environments in three countries in West Africa.<\/p>\n She says the markers have helped evolve the way they do their breeding. \u201cUsing molecular markers, we are able to identify whether the lines we are breeding have genes that confer the traits that we want,\u201d explains Eva. \u201cIt has really revolutionised our breeding program and helped it make great progress in the past three to four years.\u201d<\/p>\n In Mali, sorghum is an important staple crop. It is used to make t\u00f4<\/em> (a thick porridge), couscous, and local beers. Part of its popularity is its adaptability to various climates \u2013 in Mali it is grown in very dry environments as well as in forest\/rainforest zones. However, it is widely affected by acidic soils.<\/p>\n \u201cLow phosphorus availability is a key problem for farmers on the coast of West Africa, and breeding phosphorus-efficient crops to cope with these conditions has been a main objective of ICRISAT in West Africa for some time,\u201d says Eva.<\/p>\n \u201cWe\u2019ve had good results in terms of field trials. We have at least 20 lines we are field testing at the moment, which we selected from 1,100 lines that we tested under high and low phosphorous conditions.\u201d Eva says that some of these lines could be released as new varieties as early as next year.<\/p>\n \u201cOverall, we feel the GCP partnership with EMBRAPA and Cornell is enhancing our capacity here in Mali, and that we are closer to delivering more robust sorghum varieties that will help farmers and feed the ever-growing population in West Africa.\u201d<\/p>\n Leon notes that the work by Eva in Mali and by other African partners in Niger and Kenya is imperative for the research. \u201cJust because plants have these genes, doesn\u2019t mean they will all display aluminium tolerance or phosphorus efficiency. You still need to test and observe for these traits in the field and determine what other factors might affect plants grown in acidic soils.\u201d<\/p>\n One surprising observation that has Leon intrigued is a local sorghum variety with a phosphorus-efficiency gene that is close to where the SbMATE<\/em> gene resides in the sorghum genome. \u201cThis suggests that SbMATE<\/em>, which aids with aluminium tolerance, may also improve phosphorus efficiency. This means we could use SbMATE<\/em> markers to look for both phosphorus efficiency and aluminium tolerance,\u201d he says. Leon and Jurandir will continue to validate this result post-GCP.<\/p>\n GCP\u2019s comparative genomics projects have laid a significant foundation for further research into and breeding for tolerance to multiple plant stresses.<\/p>\n \u201cWe\u2019re in a golden age of biology where we are learning more and more about the complexities and commonalities of plants, which is allowing us to manipulate them ever so slightly to help them tolerate multiple environmental stresses,\u201d says Leon. \u201cAs a geneticist, I am extremely proud to be part of this, particularly seeing the potential impact that the basic research we do in the laboratory can have on crop improvement and the lives of people in poorer countries.\u201d<\/p>\n Although not all projects produced new and improved varieties ready for release, they are well and truly in the pipeline. Each partner institute is committed to work together and source new funding to continue on their quest to produce further products.<\/p>\n \u201cGCP has really installed in us a spirit to see this work through and expand on it,\u201d says Leon. \u201cI mean, we are now working with other countries and institutes to share what we have learnt with them and help them make the discoveries that we have. It\u2019s a credit to GCP for bringing us all together; that was a key to the success of the project. Each partner has brought their expertise to the table \u2013 genomics, molecular biology, plant breeding \u2013 and it has been great to see the impact filter into Africa and Asia.\u201d<\/p>\n In Kenya, Samuel agrees with Leon\u2019s assessment. \u201cGCP gave us an opportunity to build our expertise and start interacting with the rest of the world,\u201d he says. \u201cBut more importantly, it means that we\u2019re contributing to food security in Kenya, and that makes us really proud.\u201d<\/p>\n Although the sun is setting on GCP, work on comparative genomics projects is still in progress, with all parties still working towards delivering important new acid-beating varieties to farmers.<\/p>\n It\u2019s a cruel feature of some of the most populous areas of the world, particularly in the tropics and subtropics: acid soils. They cover a third of the world\u2019s total land area \u2013 including significant swathes of Africa, Asia and Latin America \u2013 and 60 percent of land we could use for growing food. Today […]<\/p>\n","protected":false},"author":4,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[87,88,303,148,267,154,304],"tags":[18,17,86,38,9,28,346,310,575,315,313,576,226,307,227,116,138,225,90,144,110,224,210,155,157,8,71,213,73,349,177,316,142,74,347,351,153,185,345,151,152,67,350,193,317,311,348,68,309,525],"class_list":["post-3815","post","type-post","status-publish","format-standard","hentry","category-africa","category-asia","category-comparative-genomics-in-cereals","category-genomics-2","category-maize-2","category-rice-2","category-sorghum-2","tag-crop-breeding","tag-crop-improvement","tag-drought-tolerance","tag-molecular-breeding","tag-partnerships","tag-abiotic-stress","tag-acid-soils","tag-acidic-soils","tag-africa","tag-aluminium-tolerance","tag-aluminium-toxicity","tag-asia","tag-brazil","tag-comparative-genomics-in-cereals-2","tag-cornell-university","tag-crop-genes","tag-crop-variety-release","tag-embrapa-brazil","tag-gene-discovery","tag-genes","tag-genomics","tag-icabiograd-indonesia","tag-icrisat","tag-indonesia","tag-irri","tag-jircas","tag-kenya","tag-maize","tag-mali","tag-marker-assisted-breeding","tag-marker-assisted-selection-mas","tag-moi-university","tag-molecular-markers","tag-niger","tag-phosphorus-deficiency","tag-phosphorus-efficiency","tag-phosphorus-uptake-efficiency","tag-phosphorus-poor-soils","tag-poor-soils","tag-pstol1","tag-pup1","tag-rice","tag-roots","tag-salt-tolerance","tag-sbmate","tag-soil-acidity","tag-soil-fertility","tag-sorghum","tag-zmmate","tag-zmmate1"],"_links":{"self":[{"href":"https:\/\/www.generationcp.org\/sunsetblog\/wp-json\/wp\/v2\/posts\/3815","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.generationcp.org\/sunsetblog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.generationcp.org\/sunsetblog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.generationcp.org\/sunsetblog\/wp-json\/wp\/v2\/users\/4"}],"replies":[{"embeddable":true,"href":"https:\/\/www.generationcp.org\/sunsetblog\/wp-json\/wp\/v2\/comments?post=3815"}],"version-history":[{"count":26,"href":"https:\/\/www.generationcp.org\/sunsetblog\/wp-json\/wp\/v2\/posts\/3815\/revisions"}],"predecessor-version":[{"id":5218,"href":"https:\/\/www.generationcp.org\/sunsetblog\/wp-json\/wp\/v2\/posts\/3815\/revisions\/5218"}],"wp:attachment":[{"href":"https:\/\/www.generationcp.org\/sunsetblog\/wp-json\/wp\/v2\/media?parent=3815"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.generationcp.org\/sunsetblog\/wp-json\/wp\/v2\/categories?post=3815"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.generationcp.org\/sunsetblog\/wp-json\/wp\/v2\/tags?post=3815"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}<\/a>Aluminium toxicity and phosphorus deficiency: Public enemies number one and two in the fight against acidic soils<\/h3>\n
GCP builds on past crop breeding successes<\/h3>\n
<\/a><\/a>Finding the best genes within the crop family<\/h3>\n
Extending research in sorghum and rice to maize<\/h3>\n
<\/a><\/a>Breeding for multiple stresses is a step-by-step process<\/h3>\n
<\/a>Introducing PSTOL1<\/em> into maize and sorghum<\/h3>\n
<\/a>New sorghum varieties prove their worth in the field<\/h3>\n
<\/a>Working together to improve food security worldwide<\/h3>\n
<\/a><\/a>More links<\/h3>\n
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