Faster breeding approaches for enhancing wheat production
Authors: Vikas Gupta, Satish Kumar, CN Mishra and Indu Sharma
Wheat (Triticum aestivum) is one of the important cereal crops after rice and grown over 200 m ha in different climatic conditions around the world. Wheat production has increased several folds from 15mt in 1960s to139.89 mt in 2013 but it needs to grow at a rate of 2-2.5% annually until 2050 to meet the ever increasing demand of growing population. However, for India the growth rate estimate is 1.5-2.0% annual increase in wheat production to fulfil growing demands. Wheat crop is grown under diverse climatic conditions in India ranging from fully irrigated to fully rainfed. Based on different ecological and crop growing conditions country is divided into six mega zones viz., Northern Hills Zone(NHZ), North Western plains Zone (NWPZ), North Eastern Plains Zone (NEPZ), Central Zone (CZ), Peninsular Zone (PZ) and Southern Hills Zone (SHZ). The productivity and quality of wheat crop is affected by several constraints viz., biotic constraints: rusts, leaf blight, powdery mildew and Karnal Bunt; Abiotic constraints: reduced water availability, increased temperature, waterlogging and problematic soils.
The prospects and challenges of each zone are different from the other, so the breeding objectives differ from each other except yield enhancement. Our country is self sufficient in production of wheat as of now but the projected demands for the 2050 is 140 mt. The jump in yield that was realised during green revolution period seems very difficult to be realised now because of yield stagnation, reduced irrigation water, diminishing area under cultivation and degraded soil health. There is a need to breed new cultivars with increased gain yield potential, efficient in water use, drought and heat tolerant, fertilizer use efficient, good end use quality and resistance to biotic stresses for ensuring gradual gains in wheat production.
The land mark variety, PBW 343 which ruled for >15 years was replaced due to its susceptibility to stripe rust in the North Western Plains Zone. After that many new wheat varieties were released but only a few became popular whereas most of them showed susceptibility after 2 or 3 years of release. Challenges and targets are so many in front of breeders and breeders are continuously working hard to face and achieve these challenges and targets. Plant breeding is the science of creating variability by crossing chosen parents and then selecting desirable plants from the segregating generations until homozygous purelines are selected. The selected purelines undergo another cycle of evaluation in preliminary agronomic trials followed by national coordinated trials evaluation and finally got released if they are high yielding and having other desirable traits. During this whole exercise most of the breeder’s material doesn’t see the light of the day. This continuous churning of germplasm results into development of new varieties and this process continues. For releasing a cultivar starting from initial crossing to final evaluation and release, it takes around 12-14 years. For reducing the time in the development and release of cultivars, use of molecular markers, doubled haploids and shuttle breeding approaches is of utmost importance. A variety of marker technologies have been developed ranging from Restriction Fragment Length Polymorphism (RFLP) to Single Nucleotide Polymorphism (SNPs) and used in locating position of genes/QTLs onto chromosomes. The known marker information is freely available and can be utilized in the targeted transfer of desired genes/QTLs into desired backgrounds in precise manner and short duration using double haploidy as well as shuttle breeding is discussed here.
Faster Wheat Breeding Approaches:
a. Marker assisted backcross breeding
b. Double haploidy
c. Shuttle breeding
a. Marker assisted backcross breeding
Mapping and tagging of agriculturally important genes have been greatly facilitated by an array of molecular marker technology. Marker assisted selection is gaining importance as it is greatly facilitating the precise transfer of genomic regions of interest and accelerating the recovery of recurrent parent genome. MAS have been greatly used for transferring the qualitative genes (simply inherited) whereas a few examples of transfer of quantitatively inherited traits are available. Marker assisted selection (MAS), which is being practised for improvement of different traits in wheat around the world for precise transfer of gene of interest in desired backgrounds. MAS have been successful in transfer of traits viz., abiotic stress tolerance, traits with low heritability, pyramiding of resistance genes, seedling traits, distinguishing between homozygotes and heterozygotes, which are otherwise difficult to transfer through conventional plant breeding. There is no question of biosafety and bioethics in the traits being transferred through MAS. The success of MAS depends upon 1) dense linkage map spanning whole length of chromomsomes 2) tight linkage between gene and associated marker 3) adequate recombination between flanking marker and rest of the genome 4) cost-effective marker analysis of large number of plants. The markers which are located within the gene of interest are the best choice for MAS followed by the markers which are in linkage disequilibrium with the gene of interest means both marker and genes are transmitted together without recombination. In contrast to simply inherited traits, the quantitative traits governed by large number of genes cannot be dissected to have a marker within the gene of interest. In case of transferring QTLs, the genomic region containing the genes should have flanking markers so that the target region can be transferred without any linkage drag. The markers can be used in tracking the transfer of target trait and recovery of recurrent parent genome in the context of MAS (Fig. 1). MAS improves the efficiency of backcross breeding when 1) the target phenotype is difficult to assay, 2) identification of the plant with less donor parent genome 3) linkage drag reduction. Transfer of a recessive gene through conventional plant breeding requires at least 6-7 backcrosses (BC) for transferring the target gene as well as to recover the recurrent parent genome. But it has been demonstrated in recent studies that plants with >90 % recurrent parent genome can be easily identified in third BC having minimum donor parent genome. Marker trait associations have been traced out by the use of molecular markers for marker aided selection from the last two decades and are still becoming popular in many countries. Wheat improvement using MAS technology is already going on in CIMMYT, Australia and USA (Eagles et a l2001). A consortium for MAS was formed in USA in 2001 with an objective of integrating molecular markers in plant breeding programmes of public sector. These programmes mainly focussed on traits like insect pest resistance genes, genes for bread and pasta making quality and these programmes were successful in developing MAS derived lines with all these traits. In Australia the MAS programmes utilized different traits particularly stress related genes leading to development of improved germplasm. Apart from this, marker assisted backcross breeding approach has been used for introgressing QTLs for transpiration efficiency and for negative selection for undesirable traits such as yellow flour colour.
A computer simulation model was designed by Australian scientists for effective and efficient MAS for wheat breeding. This involved integration of restricted backcrossing and doubled haploid breeding technology. For developing high yielding and resistant bread wheat cultivars, around 25 genes governing agronomic traits including insect pest resistance, quality and homeologous pairing have been utilized in CIMMYT wheat breeding programme. The whole genome sequence of wheat is available which will facilitate the development of molecular markers ultimately leading to isolation of agronomic important gene. These isolated genes can be used in the development of perfect markers for use in marker assisted selection programmes.
Fig 1: Proposed Marker assisted background breeding strategy in wheat for introgressing a target gene while recovering 97% or more recurrent parent genome in just two backcrosses (adapted from Randhawa et al 2009).
b. Double Haploidy
Doubled haploid technology facilitates the development of completely homozygous plants in one generation thus saving several generations of selfing in comparison to conventional methods, by which only partial homozygosity is obtained. It is an important tool for reducing time in attaining homozygosity not only for wheat breeding, but also for different aspects of its genetic studies. Wheat doubled haploids can be induced through anther culture and wide hybridization. However, in the recent years it has commonly been experienced that the wheat x maize system of haploid induction (Fig.2) is an effective and versatile tool among the available methods involving chromosome elimination. Doubled haploid also provides a way of combining and fixing the desirable features of diverse wheat genotype into common genetic background. The wheat x maize approach of doubled haploid production is used worldwide in wheat breeding programmes. The technique is a primary part of the wheat breeding methodology at the largest wheat breeding company in Australia, Australian Grain Technology Pvt. Ltd. Public sector institutes in Australia are also making use of this technique in wheat breeding e.g., Plant Breeding Institute, South Australian Agriculture and Development Institute and Agriculture Western Australia. In Canada several bread wheat varieties such as Superb, Snowbird, Alvena, etc. have been released by Agriculture and Agri Food Canada. Wheat variety Bond CL was developed by Colorado State University using wheat x maize crosses and released in 2004.
In Canada about 27 wheat cultivars have been developed using DH technique and DH cultivars accounted for more than a third of the western Canadian Wheat acreage in 2009. The cultivars with improved protein content with the introgression of GPC1 gene from Triticum dicoccoides has been developed in Canada (Lillian, Burnside and Somerset).The first durum cultivar DT801 was developed and released using doubled haploid approach.CDC Verona and Brigade cultivars having low grain cadmium have also been developed. In India, public sector institutions are now a day’s focusing and try to integrate this technique in their wheat breeding programmes. The wheat x maize system of haploid induction is in use at Punjab Agricultural University, Ludhiana and the cultivars developed using this approach are in testing phase in All India coordinated Wheat & Barley project. At DWR, Karnal this approach has been standardized and is now in use for doubled haploid production. Wheat x Imperata cylindrica system of haploid induction system has been effectively utilized at CSKHPKV, Palampur University. Another approach for haploid induction through genetic engineering of the centromeric region was developed by Ravi & Chan (2010). Cenh3 a kinetochore protein was first disabled by mutation and the altered version was then inserted by genetic transformation. In such plants, this novel CENH3 protein is also disabled but only to such an extent that its chromosome segregating function is maintained, while defective kinetochores cause elimination of this chromosomal set during mitotic divisions in zygotic cells. To achieve haploid induction, therefore, the method requires inactivation of the endogenous CENH3 gene by mutation or RNAi interference and the insertion of an additional gene coding for the CENH3 variant. The authors claim that another feature of this system is that the 'inducer line’ (line with the altered centromeric gene) can be used to induce either maternal or paternal haploids by crossing the mutant with female or male wild-type plants. In addition to varietal development through DH technique, mapping population can be generated which can facilitate identification and mapping of economically important traits. Whole genome mapping in a wheat doubled haploid population using SSRs and TRAPs and the identification of major QTLs associated with the traits of days to heading on chromosomes 5A and 5B, plant height on chromosomes 4D and 5A, and spike characteristics on chromosomes 3D, 4A, 4D, 5A and 5B (Chu et al., 2008). Seven consistently expressed QTLs were detected for all the traits tested for seedling root traits in a doubled haploid wheat population under different water regimes. One region in the interval Xgwm644.2-P6901.2 on chromosome 3B contained 9 QTLs affecting most root traits (Liu et al., 2013). Development of saturated linkage maps have also been carried out in doubled haploid populations. DH can also facilitate mutation breeding studies as mutations can be fixed in the first generation after mutagenic treatment. All mutated traits are immediately expressed, allowing screening for both recessive and dominant mutants in the first generation. Mutagenic treatment is applied to dormant seeds that, on germination and flowering, produce M1 gametes, which are used as donor material for haploid culture.
Fig.2. Steps involved in doubled haploid production using wheat x maize system
C. Shuttle breeding
Development of cultivars using conventional breeding usually takes around 12-14 years. In 1940, the shuttle breeding concept was started by Dr N E Borlaug for reducing the time in development of varieties by taking winter crop in Obregon and summer crop in Toluca. Similar to this, in India main crop is taken during normal season in winter and the off season or summer crop at Wheat season nursery Dalang Maidan, Lahaual-Spiti, a regional station of DWR, Karnal or at IARI, regional station, Wellington. These summer locations serve the purpose of advancing generation as well as corrective crossing. In addition to this, advanced breeding materials can be screened against natural incidence of biotic stresses (rusts, powdery mildew and loose smut) at these locations. Selections can be made for these biotic stresses and in this way two crops can be taken ultimately reducing the time in the development of cultivars. Shuttle breeding approach has become a regular feature at DWR, Karnal as well of other wheat breeding centres in India.
A large number of genes of economic importance have been tagged and mapped onto wheat chromosomes. With the release of draft sequence of wheat more number of markers will help in further narrowing down the region of interest of these genes ultimately leading to development of perfect markers. These perfect markers can be utilized using integrated approach of MAS, doubled haploids and shuttle breeding for developing better high yielding, disease resistant genotypes in shorter time frame as compared to conventional plant breeding.
1. Harpinder S. Randhawa, Jasdeep S. Mutti, Kim Kidwell, Craig F Morris, Xianming Chen and Kulvinder S. Gill (2009) Rapid and Targeted Introgression of Genes into Popular Wheat Cultivars Using Marker-Assisted Background Selection. PLoS ONE 4(6). 1-11
2. Maruthachalam Ravi and Chan Simon W L (2010). Haploid plants produced by centromere-mediated genome elimination. Nature 464: 615-618.
3. Chu C G, Xu S S, Friesen T L and Faris J D (2008). Whole genome mapping in a wheat doubled haploid population using SSRs and TRAPs and the identification of QTL for agronomic traits. Mol Breeding , Vol. 22(2):251-266.,
4. Xiulin Liu, Runzhi Li, Xiaoping Chang, Ruilian Jing (2013) Mapping QTLs for seedling root traits in a doubled haploid wheat population under different water regimes. Volume 189 (10): 51-66.
5. J. Dubcovsky (2004) "Marker-assisted selection in public breeding programs: the wheat experience. Crop Science. 44 (6), 1895-98.
6. Eagles HA, Bariana HS, Ogbonnaya FC, Rebetzke GJ, Hollamby GJ, Henry RJ, Henschke P and Carter M (2001). Implementation of markers in Australian wheat breeding. Australian Journal of Agricultural Research, 52:1349-1356.
About Author / Additional Info:
I am working as a Scientist in Indian Institute of Wheat and Barley Karnal, Haryana under ICAR, New Delhi.