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Breeding For Root Traits: Improving The Forgotten Trait

BY: Om Prakash Patidar | Category: Genetics | Submitted: 2016-05-22 06:24:03
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Article Summary: "Roots are the very important component of the plant that helps in absorbing nutrients and water from the soil which ultimately determines the yield and productivity. But this trait is neglected in breeding programmes. It is important to genetically dissect this complex, multicomponent trait to develop elite varieties to meet foo.."

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Breeding For Root Traits: Improving The Forgotten Trait
Authors: Om Prakash Patidar, Sunil Kumar and Arvind Nagar

Crop Root Structure And Function

Their main function of a plant root is to get the water and nutrients contained in soils that are required for productivity. Several factors in soils lead to spatially and temporally heterogeneous conditions, including physical properties determined by mineral nutrient content, water content, biotic factors such as soil microbial populations and the plant communities that inhabit in a particular location. The spatial heterogeneity of soils makes a complex problem to study roots under field conditions. Because of their unique role in extracting both water and minerals from soils that are essential for plant and animal nutrition.

Why root genetic improvement important to us?
1. For improving nutrients efficiency

Unused fertilizer is washing off fields into rivers, poisoning coastal waters. Nitrogen use efficiency (NUE) for cereals production is around 33% worldwide. The remaining N from fertilizer is lost to the atmosphere or leached into the groundwater and other freshwater bodies, which is causing serious N pollution and becoming a threat to global ecosystems (Nosengo, 2003). On the other hand, nutrients deficiencies are most frequently encountered in agriculture practices. For example, low phosphorous levels in soils are the major constraint for crop production. Only 12-21 per cent of the P supplied in fertilizers is available to plants. The development of varieties with an improved ability to utilize this large but hardly plant-available P pool could bring a more sustainable solution than relying on fertilizer application alone.

2. For enhancing tolerance to abiotic stresses

Drought, one of the most severe abiotic stresses which are limiting crop productivity in the world, and posses a serious danger to the sustainability of crop yields in rainfed agriculture systems. Another severe abiotic stress is soil salinity is in agriculture worldwide. About 20% of the world's cultivated land and nearly half of all irrigated lands are affected by salinity. A high salt stress condition disturbs homeostasis in water potential and ion distribution. The 'exclusion' of Na+ and Cl- by roots is of paramount importance for the plants growing in saline soils. High-affinity K+ transport systems are also essential for preventing toxicity by Na+. Therefore, one way to develop plant cells with improved salt tolerance is to increase K+ uptake activity of the cells, while keeping Na+ out during salt stress. Developing salt tolerance varieties is also a task for crop breeders in the future.

3. For Increasing productivity

Among essential nutrient elements required, inorganic carbon is absorbed mainly by leaves in the form of CO2 and the other essential mineral elements through root surface from the soil. As described in the report by Zhang et al. (2009), the high grain yield was mainly due to a larger sink size as a result of a larger panicle. The low percentage of filled grains was closely associated with a quick decreased root activity during grain filling. Further research is needed to understand the mechanism involved in the low percentage of filled grains and yield fluctuation and to improve the yield performance in elite hybrid lines. The yield of superior varieties can further be increased by an increase in filled grains through enhancing root activity during grain filling (Yang, 2011).

What should the root architecture be?

A robust plant root system is a necessary factor for vegetative and reproductive growth, but progress in using root as a trait to boost crop productivity has been slow (Comas et al., 2013). Suitable root ideotypes for improving plant productivity is by enhancing soil mineral resource capture and by reducing root lodging. To increase nitrogen and water use efficiency a steep-deep-cheap ideotype has been proposed for crops grown under certain conditions. This model integrates deep rooting for water, root angles required for nitrate recovery, and nutrient acquisition and a decrease in root cortical cells through the development of aerenchyma to reduce the carbon cost of root maintenance. Root architecture ideotypes includes complex, interconnected and multicomponent traits. The strategies to manipulate architecture should be specific to crop, which is challenging task because a tool kit of several genes may be required.

Some Genetic Know-Hows Of Root Systems

Although genetic and molecular dissection of root traits has been done in many crops like rice, maize, wheat, and soybean, but is still lot more is yet to be done. In maize, this includes an auxin responsive LOB domain transcription factor Rootless concerning Crown and Seminal root (RTCS) and its downstream target Auxin Response Factor (ARF34), which control nodal root formation in monocots. The short lateral roots 1 and 2 (slr1, slr2) and lateral root 1 (lrt1) loci are found to control lateral root development in maize; however, the underlying genes have not been cloned (Hochholdinger et al., 2005). There is also multiple root structure QTLs recorded in maize, which control architecture and yield stability across multiple genetic back- grounds and in several different water regimes. Rice root structure is controlled by several genes including: the auxin regulated Adventitious and Crown Rootless ARL1; CRL1, which encodes a LOB domain transcription factor conserved across monocots and dicots. Root hairs are unicellular functional units of roots, so modulating root hair number and length is an alternate way to improve root function depending on the soil type. Since several genes are conserved between rice and Arabidopsis so it offers an opportunity to improve root traits using these genes in several other crops too. To study tape root system of dicots Arabidopsis is a model plant.

Efforts To Manipulate RSA In Crops

The most of the progresses has been done in rice that may be by over expression of transcription factors OsNAC5/9 and OsMYB2, the receptor kinase PSTOL1, the G-protein coding Root Architecture Associated (OsRAA1) and the identification of the DRO1 allele. It is important to note here that these genes which are related to RSA are also improving the nutrient use efficiency of crops. Two best examples of where genes have been identified that confer changes in root architecture are DRO1 and PSTOL1. In rice where root angle and rooting depth can now be targeted by breeding or using transgenic approaches using DRO1 to achieve the steep-deep ideotype. A major QTL for phosphorus deficiency tolerance in rice PSTOL1 encodes a receptor-like kinase that maps that has been shown to increase root biomass.

Problems And Prospects

Although, root is an important plant part which greatly determines the yield and productivity of the plants a very less efforts have been made to understand its genetic basis compared to above ground parts. First of all, the phenotyping of roots is very difficult. Most of the methods include destructive methods. In situ phenotyping is very important to know the temporal and spatial characteristics of the roots but a very less methods are available and are of not with that level of resolution which could help in getting better conclusions. These methods are time consuming and laborious. Soil cultures are available which mimics the soil environment but are not up to the mark.


1. Comas, L. H., 2013, Root traits contributing to plant productivity under drought. Front. Plant Sci. 4: 442-444.

2. Hochholdinger, F. and Tuberosa, R. 2009, Genetic and genomic dissection of maize root development and architecture. Curr. Opin. Plant Biol. 12: 172-177
3. Nosengo, N., 2003. Fertilized to death. Nature,425: 894-895.
4. Yang, J. C., 2011. Relationships of rice root morphology and physiology with the formation of grain yield and quality and the nutrient absorption and utilization. Sci. Agr. Sinica.44: 36-46.
5. Zhang, H., Xue, Y., Wang, Z., Yang, J., Zhang, J., 2009. Morphological and physiological traits of roots and their relationships with shoot growth in super rice. Field Crops Res. 113: 31-40.

About Author / Additional Info:
Author is a PhD student in Genetics Division of Indian Agricultural research Institute, New Delhi, India

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