Pre‐breeding refers to all the activities designed to identify desirable characteristics and/or genes from un-adapted materials that cannot be used directly in breeding populations and to transfer these traits to an intermediate set of materials that breeders can use further in developing new varieties.
Crop wild relatives have a high level of genetic diversity with rare alleles that enabled them to survive in natural and adverse environments. Most plant breeders fear in using exotic or un-adapted material due to its initial detrimental effects like linkage drag on elite breeding material. It is a necessary first step in the use of diversity arising from wild relatives and other un-adapted materials.
Pre-breeding attempts to reset the genetic diversity of crops by reintroducing genetic variation that has been left behind. The Compound annual growth rate (CAGR) of major wheat breeding programs across the globe is very low, particularly in recent years. It is feared that unless new diversity is infused into the breeding programs, we may face catastrophic reductions in productivity if the climate turns adverse.
Wild species and exotic cultivated germplasm holds a wealth of alleles. If we can able to find them (alleles of interest) then it can be helpful to break yield barriers and enhance tolerance to stresses and stability.
Bread wheat (Triticum aestivum L.) belongs to the tribe Triticeae, is one of the most important food crops, cultivated on about 220 million ha, meeting the food requirement of one-third of the global population and providing 20% of the global caloric requirements (Rasheed et al., 2018).
Global food requirement is increasing alarmingly and is further compounded by the challenges of climate change, stagnant wheat yields in many countries, outbreaks of new pathogen/pest races, and invasive weed species that delay progress and pose serious threats to world food security.
It is therefore prudent to approach the challenges of food security by placing emphasis on utilizing untapped gene pool.
Utilization of untapped gene pool in wheat
The selection efficiency in any breeding programme for higher yield depends upon the variability available in germplasm. Due to continuous domestication and directional selection pressure, the variability is narrowing down. Keeping in this view, germplasm should be diversified to contain the boom and bust kind of situation and to increase the yield potential in wheat.
The diversity present in the un-adapted gene pool has provided many useful traits now deployed widely in elite germplasm, and expanded use of this germplasm resource is seen as crucial to accelerating the rate of genetic gain in plant breeding. The success of using the D genome (Aegilops tauschii) derived user friendly genetic stocks (synthetic wheats, SH or SHW) speaks the potential of pre-breeding technology.
Advanced derivatives of these materials have positively impacted yield and its attributes, increased micronutrient content, provided novel genes for resistance to major biotic and abiotic stresses, and improved the processing quality of elite varieties (Ogbonnaya et al., 2013).
Many leading varieties in Europe (e.g. ‘Robigus’) are derived from unknown introgressions from T. dicoccoides. Similarly, an introgression from Ae. umbellulata saved US wheat production from leaf rust in 1960; and a gene from Ae. Ventricrosa conferring resistance to eyespot has been exploited in breeding programmes (Garcia-Olmedo et al., 1977).
Challenges associated with pre-breeding
- Cross incompatibility in distant hybridization
- Stability barriers and difficulties in chromosome pairing in hybrids
- Linkage drag
- Hybrid inviability and sterility
- Small sample size of inter-specific hybrid population
- Restricted genetic recombination in the hybrid population
- Lack of characterization and evaluation data
- Long duration
Recent advances in rapid utilization of un-adapted germplasm
One of the major constraints in using wheat genetic resources in breeding programmes is the time factor associated with difficulties in evaluating wheat genetic resources with widely different phenologies of growth habit, flowering time and height.
Even if useful characteristics can be identified, the difficulties of transferring desirable traits into cultivated species are considerable, often requiring embryo rescue and cytological expertise.
The time required to transfer traits from wheat genetic resources and to enable their use in breeding often may exceed that in conventional breeding programmes. The recent advances in the development of high-throughput, time-saving methods fall into five categories:
1. Rapid generation advancements:
Shuttle breeding strategy, which moves germplasm between contrasting environments, will help screening for a range of traits such as photo-period sensitivity, heat tolerance and arrangement of important biotic and abiotic stresses. Double haploids rapidly bring about homozygosity. A new generation advancement method called ‘speed breeding’ uses constant light and precisely controlled temperature to accelerate plant growth and development.
2. Rapid gene cloning through mutation and genomics:
The three-step method (MutRenSeq) that combines mutagenesis with exome capture and sequencing provided a rapid way to clone R genes from wheat wild relatives, a classical example being discovery of Sr22 from monococcum and Sr45 from Ae.tauschii.
3. High-throughput genotyping and phenotyping platforms:
In recent years, there have been rapid advances in high throughput genotyping arrays or GBS. It is now possible to genotype hundreds of samples for high-density markers within a couple of days.
4. High-throughput marker-assisted selection strategies:
Progress in developing high-throughput single marker genotyping was relatively slow compared to current high-density genotyping platforms. Single marker genotyping is very important for wheat pre-breeding programmes because breeders are much more interested in deploying specific alleles from wheat genetic resources.
5. Rapid gene editing technologies:
Recent development of efficient and specific CRISPR / Cas9-mediated gene editing methods with decreased off-target mutations in a short period of time is a major focus for researchers.
One of the important advantages of CRISPR / Cas9 RNP - mediated genome editing is elimination of transgene integration and the small DNA insertions that can be generated. This is highly desirable option for public acceptance of genome-edited plants and holds significant potential for exploitation of wheat genetic resources in reduced time periods.
As the need to incorporate wild genetic diversity grows along with threats of climate change and the narrowing genetic base of wheat, it is increasingly important that we understand how wild species are being efficiently used to improve wheat.
Pre-breeding is an efficient tool to bring valuable genes from un-adapted wild gene pool to improve wheat varieties. A closer look at the current state of wheat genetic resources use reveals persisting challenges, as well as significant opportunities for harnessing their value.
Gopalareddy K*, BS Tyagi and Kailash Prajapat1
Address: ICAR-Indian Institute of Wheat and Barley Research, Karnal-132001 (Haryana)
1ICAR- Central Soil Salinity Research Institute, Karnal-132001 (Haryana)