Rice production constraints in various ecologies of rice cultivation.
Abstract
Increasing incidences of multiple abiotic stresses together with increasing population are the major constraints to attain the global food security. Rice, the major staple food crop is very much prone to various abiotic and biotic stresses, which can occur one at a time or two or more together in a single crop growing season and adversely affects the rice production and productivity. The devastating effect of multiple stresses on rice crop is much more erratic and complex leading to higher losses in the crop grain yield. The concurrent occurrence of multiple streeses can destroy rice production in many of the rainfed areas of South and Southeast-Asia. Genomics-assisted breeding strategies have been instrumental in introgression of various major effect QTLs/genes into rice mega varieties and have proven successful in achieving the desired level of tolerance/resistance to various abiotic stresses in diffferent crop species. Keeping the present scenario of changing climate in mind, the chapter discusses the recent past success in combining tolerance to two or more abiotic stresses in mega rice varieties applying genomics-assisted breeding and development of high-yielding climate resilient rice through stacking of multiple genes/QTLs, which can withstand in a cascade of multiple stresses occurring regularly in rainfed environments.
Keywords
- abiotic stress
- biotic stress
- genomic-assisted breeding
- pyramiding
- QTLs
- rice
- yield
1. Introduction
Global warming and the changing climatic conditions lead to the concurrence of multiple abiotic and biotic stresses individually/or in combination [1, 2] thus adversely affecting the rice crop growth and yield [3]. The changing climate, more and more extreme weather events are increasing the probability of simultaneous multiple abiotic stresses, including extra pressure from biotic stresses. Abiotic and biotic stresses reported to have significant negative impact on rice crop survival, growth, development and yield in most parts of the world, especially the Asia and Africa [4, 5]. The abiotic stresses such as drought, salinity, cold, high temperature and heavy metals are known to influence the occurrence of biotic stresses [6, 7, 8]. The combined effect of multiple stresses may resulted the minor pests to become the potential threats in the coming future [1, 9, 10].
The rice farming is practiced in various diverse ecological zones. The rice cultivation system in diiferent growing areas are mainly depends upon various factors such as available water, soil type, and the prevailing monsoon. Rice production faces various constraints in various ecology of rice cultivation (Table 1). Rice crop faces multiple stresses during different stages of its growth and development and around 70% reduction in yield was reported due to the occurance of abiotic stresses at different stages of growth and development [5]. Similarly, the major biotic stresses such as bacterial leaf blight, blast, brown plant hopper, brown spot, sheath blight and gall midge reported to impart severe crop yield losses or even complete crop failure during infestation [4]. The growth of rice yield has deteriorated from 2.3% per year during 1970s–1980s to about 1.5% during 1990s, and to <1% in the first decads of this present century [11]. Although the rice production has improved considerably over time but it is not sufficient to cope with the increasing demand globally [12]. The annual shortage of rice is expected to rise from 400,000 tons in 2016 to around 800,000 tons by 2030 [13].
Ecosystem | Source of water | Constraints |
---|---|---|
Upland | Rainfall | Drought, blast, weeds, low soil fertility, Fe toxicity, soil nematode problem, lodging |
Rainfed shallow lowland | Rainfall, water table | Lack of assurred irrigation, frequent drought, blast, bacterial leaf blight |
Rainfed medium lowland | Rainfall, water table | Lack of assurred irrigation, drought, flood, drought and flood in same or different season, bacterial leaf blight, brown plant hopper, gall midge |
Rainfed deep lowland | Rainfall, water table, flood water | Lack of assured irrigation, fragile and low productivity, Prevailing abiotic stresses such as flood, salinity, Biotic stresses such as bacterial leaf blight, gall midge, brown plant hopper |
Irrigated | Irrigation | Salinity, bacterial leaf blight, brown plant hopper |
As crop plants are immobile, they have to respond to the different abiotic and biotic stresses in the field itself. Breeding efforts in developing tolerance for single stress such as drought, heat, salinity, cold, insect and pathogen or a single stress type viz. abiotic or biotic may be tricky because plants may respond differentially to different or simultaneous occurance of stresses. The increase in resistance/tolerance to one type of stress may be at the cost of resistance/tolerance to another stress [14]. Breeding of high yielding multiple stress tolerant/resistant rice varieties with better grain quality is the urgent need of the hour since many decades [15]. Improvement of germplasm involving improved donors free from undersirable linkage, identification and introgression of genomic regions after validation involving recent advances in genomics-assisted breeding has provided opportunity to combat the challenges arising due the occurance of multiple stresses [16]. An integrated genomics-assisted breeding approach to introgress desirable genes/QTLs conferring tolerance/resistance to major abiotic and biotic stresses in addition to improved yield and quality will help to combat the present situation [16, 17, 18, 19, 20]. The commercial use of QTLs/genes-conferred multiple stress tolerant/resistant rice varieties provides an effective, economical and environment friendly approach to protect the crop yield and productivity. In past few years, the identification of genomic regions associated with drought, submergence and heat tolerance and introgression and pyramiding of these regions applying markers assisted selection/backcross approach have successfully led to the development of drought or flood tolerant version of some of the mega varieties such as Swarna, IR64 and Sambha Mahsuri. Some of these developed genomics-assisted derived breeding lines have been released as varieties in various countries of South Asia and South East Asia for cultivation.
2. Biotic stresses
2.1 Bacterial blight
Rice crop is most vulnerable to bacterial blight (BLB) caused by
2.2 Blast
Rice blast (
2.3 Brown plant hopper
Brown plant hopper (
2.4 Gall midge
The Asian rice gall midge (
3. Abiotic stresses
3.1 Drought
Among the abiotic stresses, drought is one of the most disruptive, and risky events of the ongoing climate change that affect millions of people every year across the world. Depending upon the intensity and pattern of rainfall, drought can occur from few days to few months or even to years [70]. The development of high yielding drought-tolerant rice varieties is the final goal of rice breeders to reduce the yield losses due to drought and to ensure the projected world food production. However, the development of drought-tolerant rice varieties is immensely tough due to the complex quantitative nature of trait [71, 72]. The selection of lines under differential level of drought and due to the occurrence of drought at different stages [73, 74, 75] is again not an easy task. In addition, the strong GxE interactions and low heritability of traits such as grain yield also add to the difficulty of the task [76]. Cost-effective modified breeding strategy involving combined phenotyping and genotyping selection approaches in the development and screening of large segregating populations covering high genetic variation have led to the successful identification of 12 major effect QTLs (
3.2 Salinity
Salinization of soil is an another important crises the world is facing nowadays. Salty soil which is widely distributed across the world is major factor of rice yield reduction. The salt affected land in India accounts for 6.73 mha (million heactare) which is predicted to increase to 16.2 mha by 2050 [86, 87]. The complexity of salt tolerance mechanisms limits the development of high yielding salt tolerance rice varieties [88]. Salinity stress reported to affect rice grain yield from 20 to 100% depends on the severity of the stress and the duration of stress exposed to the rice crop [89]. Fortunately, the exiting wide genetic variability in rice germplasm in response to soil salinity stress makes possible to develop salt tolerant rice varieties [90, 91, 92]. The identification and introgression of the trait (s)/genomic regions of interest are the well-known approaches for the development of salinity tolerant varieties [93, 94]. Marker assisted breeding approaches have been proven successful in developing new improved, high yielding salt tolerance rice varieties [95, 96, 97, 98, 99, 100].
3.3 High and low temperature
Global changes in the climate conditions and increasing greenhouse gas emission led to a rise in earth’s surface temperature in some past decades, and the temperature is predicted to rise by 2 to 4°C by 2050 [101]. The high temperature duration of 3–5 days, 5–7 days and above 8 days is generally considered as mild, moderate and severe heat injury, respectively [102] while low temperature ranged from 0 to 15°C and <0°C categorized as chilling and freezing stress, respectively. Over the past few decades, extensive efforts have been made in identification of genes/QTLs improving heat [103, 104, 105] and cold tolerance [106, 107] in rice, which are very complex trait.
4. Marker-assisted pyramiding of multiple QTLs/genes for abiotic/biotic stresses
The challenges from the climate change scenario require the development of climate-adapted rice varieties that combine the tolerance of various abiotic and biotic stresses to better sustain yield losses from unpredicted climate-related events. Recent developments in the identification of major QTLs/genes for drought, submergence, salinity, bacterial blight, brown plant hopper, gall midge, and blast and the successful introgression of identified QTLs to develop improved varieties tolerant of different individual stresses indicate that, with the advent of new marker technology, the development of varieties that combine tolerance of the various abiotic and biotic stresses prevalent in any region is feasible. Such varieties once developed can help farmers overcome yield losses and better farm income under the changed climatic conditions.
The identification of major effect QTLs for the grain yield under drought
Marker assisted gene pyramiding is an effective breeding strategy to transfer more than one tolerance/resistance genes into a single rice line in order to achieve durable and broader resistance level which can prevent the breakdown of tolerance/resistance against specific races/pathogens [115]. Pyramiding of BLB resistant genes such as
Rice lines pyramided with multiple disease resistance genes (
Variety | QTLs/gene combinations | Targeted trait | Targeted country | Year of release |
---|---|---|---|---|
DRR dhan-42 | Drought | India | 2014 | |
Yaenelo 4 | Drought | Myanmar | 2015 | |
Yaenelo 5 | Drought | Myanmar | 2016 | |
Yaenelo 7 | Drought | Myanmar | 2016 | |
CR dhan-801 | Drought + flood | India | 2017 | |
Bahuguni dhan-2 | Drought + flood | Nepal | 2017 | |
Bahuguni dhan-1 | Drought + flood | Nepal | 2017 |
5. QTLs/gene pyramiding through multiple parents crossing
To tackle the multiple problems of rice cultivation under ongoing climate change, a high yielding climate smart new rice lines with superior grain quality is the urgent need to intensify the sustainable rice production. Genomics-assisted breeding (GAB) was attempted to introgress and assemble multiple QTL/genes-
An increase in rice productivity through introgression of multiple traits which can improve rice adaptability under dry direct seeded (DSR) and additionally carrying traits for abiotic/biotic stresses looks a promising breeding strategy to adapt with changing climate, limited water and labor resources and increase rice yield under mechanized DSR conditions. QTLs for traits that increase adaptability to direct seeded rice conditions such as root traits [nodal root number (
5.1 Steps in multiple-trait breeding
Three steps involved in multiple traits introgression scheme, (a) assemble first (b) line fixation and (c) line evaluation. In assemble first step, a complex crossing scheme utilized in transferring the desirable alleles/traits from all the targeted parents aimed to accumulate one copy of all targeted genes/QTLs in a single genotype. In line fixation step, gene based/SSRs/linked markers were utilized in each generation from F2 to F6 generation for tracking the presence of desirable alleles of targeted QTLs/in order to find homozygous plants carrying all the targeted QTLs/genes. Phenotyping of the homozygous lines for the targeted traits were performed in line evaluation step and proceed further for multilocation testing of promising lines in the targeted environments. The detailed description on traits, donors, QTLs/genes and markers associated that were used in genomic-assisted breeding program for the development of climate resilient lines at IRRI, Philippines (Table 3).
Trait | Donor | QTLs/genes | Markers (SNPs/Indels/SSRs/gene based markers) | Reference |
---|---|---|---|---|
Biotic stress | ||||
Blast | WHD-1S-75-1-127, Tadukan, IRBL9 | [40, 117, 121] | ||
Bacterial leaf blight | IRBB60, | [117, 122] | ||
Brown plant hopper | Rathu Heenati | RM589,RM586,RM190, RM8213, RM16556, RM586, RM589, RM190, RM7639, RM19311(linked markers) | [14, 117, 123] | |
Gall midge | Abhaya | GM4_LRR-del_F, GM4_LRR-del_R | [49, 117, 124] | |
Abiotic stress | ||||
Drought + submergence | IR96322-34-223-B | [19, 117] | ||
Drought | IR74371-46-1-1 | RM28099, RM28166, Indel 8, SnpOS00483(G), SnpOS00484(A) | [77, 117] | |
Cold | IR 83222-8-1-1-1-1-1-1-1, IR 66160-121-4-4-2, HGKN | [125, 126] | ||
Heat | N22/IR64 | id4005120, id4011562 | [104] | |
Salinity | Pokkali/IR29 | G11A, AP3206, RM3412, RM493 | [110, 127] |
5.2 Challenges in multiple-trait breeding
The complex breeding program that targets combining tolerance of various abiotic and biotic stresses together in the various genetic backgrounds is unpredictable and more research is needed as such, little is known about the effect that each gene/QTL on the others. However, it is highly assumed that most of the QTLs/genes should work in an additive manner, as far as the targeted QTLs/genes are either located on different chromosomes or in different regions of the same chromosomes. Genomic interactions play a significant role in deciding the performance of introgression lines pyramided with various drought grain yield QTLs in rice [128, 129, 130, 131]. In some cases, epistatic interactions between different loci can enhance or reduce the effect of some of the genes/QTLs. Under such a situation, as an alternative strategy of identifying and advancing lines with different combinations of genes/QTLs- six, seven, or eight for different stresses and showing higher grain yield under nonstress conditions will also be selected and the best combinations that will show tolerance of a maximum number of abiotic and biotic stresses and the highest yield advantage will be advanced for testing. Plants carrying maximum number QTLs/gene but having negative interaction with grain yield and showing inferior plant type can be rejected for further advancement.
Maintenance of larger population size could also be a feasible strategy which can allow to select rare recombinants having maximum number of targeted QTLs/genes and also free from undesirable linkages. In previous studies, drought tolerant rice lines were developed through successful breakage of the linkages between loci for tolerance to drought and undesirable traits by fine mapping and maintain huge population size [132].
6. Role of genomic selection in multiple-trait breeding
Genomic selection (GS) in crop plants facilitates the rapid selection of superior accessions/genotypes and accelerate the breeding cycle targeted for higher genetic gain. It aims to use the genome-wide markers to predict the effects of all associated loci. The developed best prediction model is applied to the tested breeding material which has been charactized only genotypically but not phenotypically. The breeding estimated value called as GEBV (genomic estimated breeding value). The parental lines with higher GEBV can be selected as the candidate lines for future breeding programs. Most of the previous studied in cereal crops has shown great potential for GS to enhance the selection for grain yield and yield related traits [133, 134]. Multi trait genomic selection can be also implemented on phenotypic data of multiple traits
7. Conclusions
To solve the global issue of food security in the era of changing climate, novel approaches involving successful stacking of multiple genes/QTLs in a single rice line utilizing strategic phenotypic-genotypic selection could provide opportunity targeting genetic gain in rice. New advances in hybridization stratgies, genomics, marker development, and sequencing permitted the opportunity to create muti-gene carrying high-yielding rice varieties to combat multiple stresses. The development of rice varieties carrying multiple QTLs/genes in homozygous conditions can address the production constraints faced due to both biotic and abiotic stresses simultaneously. These stress-tolerant rice varieties with desired grain quality can greatly help farmers in improving productivity under multiple stress conditions.
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