Phenotyping for drought tolerance in grain crops: when is it useful to breeders?

2012 ◽  
Vol 39 (11) ◽  
pp. 851 ◽  
Author(s):  
J. B. Passioura

Breeding for drought tolerance in grain crops is not a generic issue. Periods of drought vary in length, timing and intensity and different traits are important with different types of drought. The search for generic drought tolerance using single-gene transformations has been disappointing. It has typically concentrated on survival of plants suffering from severe water stress, which is rarely an important trait in crops. More promising approaches that target complex traits tailored to specific requirements at the different main stages of the life of a crop, during: establishment, vegetative development, floral development and grain growth are outlined. The challenge is to devise inexpensive and effective ways of identifying promising phenotypes with the aim of aligning them with genomic information to identify molecular markers useful to breeders. Controlled environments offer the stability to search for attractive phenotypes or genotypes in a specific type of drought. The recent availability of robots for measuring large number of plants means that large numbers of genotypes can be readily phenotyped. However, controlled environments differ greatly from those in the field. Devising pot experiments that cater for important yield-determining processes in the field is difficult, especially when water is limiting. Thus, breeders are unlikely to take much notice of research in controlled environments unless the worth of specific traits has been demonstrated in the field. An essential link in translating laboratory research to the field is the development of novel genotypes that incorporate gene(s) expressing a promising trait into breeding lines that are adapted to target field environments. Only if the novel genotypes perform well in the field are they likely to gain the interest of breeders. High throughput phenotyping will play a pivotal role in this process.

Genes ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 1026 ◽  
Author(s):  
K. N. S. Usha Kiranmayee ◽  
C. Tom Hash ◽  
S. Sivasubramani ◽  
P. Ramu ◽  
Bhanu Prakash Amindala ◽  
...  

This study was conducted to dissect the genetic basis and to explore the candidate genes underlying one of the important genomic regions on an SBI-10 long arm (L), governing the complex stay-green trait contributing to post-flowering drought-tolerance in sorghum. A fine-mapping population was developed from an introgression line cross—RSG04008-6 (stay-green) × J2614-11 (moderately senescent). The fine-mapping population with 1894 F2 was genotyped with eight SSRs and a set of 152 recombinants was identified, advanced to the F4 generation, field evaluated with three replications over 2 seasons, and genotyped with the GBS approach. A high-resolution linkage map was developed for SBI-10L using 260 genotyping by sequencing—Single Nucleotide Polymorphism (GBS–SNPs). Using the best linear unpredicted means (BLUPs) of the percent green leaf area (%GL) traits and the GBS-based SNPs, we identified seven quantitative trait loci (QTL) clusters and single gene, mostly involved in drought-tolerance, for each QTL cluster, viz., AP2/ERF transcription factor family (Sobic.010G202700), NBS-LRR protein (Sobic.010G205600), ankyrin-repeat protein (Sobic.010G205800), senescence-associated protein (Sobic.010G270300), WD40 (Sobic.010G205900), CPK1 adapter protein (Sobic.010G264400), LEA2 protein (Sobic.010G259200) and an expressed protein (Sobic.010G201100). The target genomic region was thus delimited from 15 Mb to 8 genes co-localized with QTL clusters, and validated using quantitative real-time (qRT)–PCR.


2021 ◽  
Vol 11 ◽  
Author(s):  
Anjuman Arif ◽  
Najma Parveen ◽  
Muhammad Qandeel Waheed ◽  
Rana Muhammad Atif ◽  
Irem Waqar ◽  
...  

This study was planned with the purpose of evaluating the drought tolerance of advanced breeding lines of chickpea in natural field conditions. Two methods were employed to impose field conditions; the first: simulating drought stress by growing chickpea genotypes at five rainfed areas, with Faisalabad as the non-stressed control environment; and the second: planting chickpea genotypes in spring to simulate a drought stress environment, with winter-sowing serving as the non-stressed environment. Additive main effects and multiplicative interaction (AMMI) and generalized linear models (GLM) models were both found to be equally effective in extracting main effects in the rainfed experiment. Results demonstrated that environment influenced seed yield, number of primary and secondary branches, number of pods, and number of seeds most predominantly; however, genotype was the main source of variation in 100 seed weight and plant height. The GGE biplot showed that Faisalabad, Kallur Kot, and Bhakkar were contributing the most in the GEI, respectively, while Bahawalpur, Bhawana, and Karor were relatively stable environments, respectively. Faisalabad was the most, and Bhakkar the least productive in terms of seed yield. The best genotypes to grow in non-stressed environments were CH39/08, CH40/09, and CH15/11, whereas CH28/07 and CH39/08 were found suitable for both conditions. CH55/09 displayed the best performance in stress conditions only. The AMMI stability and drought-tolerance indices enabled us to select genotypes with differential performance in both conditions. It is therefore concluded that the spring-sown experiment revealed a high-grade drought stress imposition on plants, and that the genotypes selected by both methods shared quite similar rankings, and also that manually computed drought-tolerance indices are also comparable for usage for better genotypic selections. This study could provide sufficient evidence for using the aforementioned as drought-tolerance evaluation methods, especially for countries and research organizations who have limited resources and funding for conducting multilocation trials, and performing sophisticated analyses on expensive software.


Author(s):  
Rui-Ru Ji

Common diseases or traits in humans are often influenced by complex interactions among multiple genes as well as environmental and lifestyle factors rather than being attributable to a genetic variation within a single gene. Identification of genes that confer disease susceptibility can be facilitated by studying DNA markers such as single nucleotide polymorphism (SNP) associated with a disease trait. Genome-wide association approaches offers a systematic analysis of the association of hundreds of thousands of SNPs with a quantitative complex trait. This method has been successfully applied to a wide variety of common human diseases and traits, and has generated valuable findings that have improved the understanding of the genetic basis of many complex traits. This chapter outlines the general mapping process and methods, highlights the success stories, and describes some limitations and challenges that lie ahead.


2018 ◽  
Vol 53 (3) ◽  
pp. 298-306
Author(s):  
Willame dos Santos Candido ◽  
Renato Silva Soares ◽  
Carolina Andrade Franco ◽  
Guilherme Matos Martins Diniz ◽  
Edgard Henrique Costa Silva ◽  
...  

Abstract: The objective of this work was to estimate the stability and genotypic adaptability of advanced lines and cultivars of curled green-leaf lettuce (Lactuca sativa), in different growing environments and seasons, using the REML/Blup mixed model. Ten genotypes, seven cropping environments, and two growing seasons were studied in 2015. Plant yield traits were evaluated, and data were subjected to the Selegen-REML/Blup software. Genotype stability and adaptability were analyzed using the harmonic mean of genotypic values (HMGV) and the relative performance of genotypic values (RPGV), respectively. The harmonic mean of RPGV (HMRPGV) was used to simultaneously estimate the stability, adaptability, and yield of breeding lines or cultivars. Considering the combined analysis of the two seasons for the set of traits, the lines L6, L7, and L8 were selected as promising ones and recommended for planting. The breeding lines selected for all season exhibit good yield and are considered superior to the commercial cultivars Vanda and Vera.


2012 ◽  
Vol 10 (3) ◽  
pp. 171-176 ◽  
Author(s):  
Christian A. Fatokun ◽  
Ousmane Boukar ◽  
Satoru Muranaka

Cowpea is an important grain legume crop in sub-Saharan Africa (SSA) where, on a worldwide basis, the bulk is produced and consumed. The dry savanna area of SSA is where cowpea is mostly grown under rain-fed conditions. The crop is therefore prone to drought which may occur early, mid and/or late in the cropping season. Compared with many other crops, cowpea is drought tolerant, even though drought is still a major constraint limiting its productivity in SSA. Increasing the level of drought tolerance in existing cowpea varieties grown by farmers would enable them to obtain more and stable yield from their cowpea fields. As a first step towards enhancing drought tolerance in existing cowpea varieties, 1288 lines were selected randomly from cowpea germplasm collections maintained at the International Institute of Tropical Agriculture, and evaluated for their drought tolerance at Ibadan. Drought was imposed by withdrawal of irrigation from 5 weeks after sowing. On average, drought reduced the number of days to flower by 12 d, and the mean grain yield per plant was also reduced by 67.28%. A few of the cowpea lines stayed green for up to 6 weeks after irrigation was stopped, even though some of these produced no pods when the study was terminated. Further evaluation in the screenhouse of 142 selected drought-tolerant lines helped to identify six lines that could be potential parents for developing breeding lines with enhanced drought tolerance.


2012 ◽  
Vol 60 (4) ◽  
pp. 417-432 ◽  
Author(s):  
R. Mohammadi

The main objective of this study was to evaluate the genetic gain for grain yield, yield attributes and drought tolerance of 11 durum breeding lines and also to compare it with one modern cultivar and two durum and bread wheat landraces in contrasting environment groups in a period of four cropping seasons (2005–09) within the Iran/ICARDA joint project for moderately cold rainfed areas of Iran. The significant genotype × year interaction indicated that the average yield performance of genotypes across environments was not consistent over the years. Genetic gain (%) for grain yield was distinguishable between the stressed and non-stressed environments. A positive genetic gain (27.7 to 23.9%) was observed in the non-stressed environment and a negative genetic gain (−11.5 to −24.1%) in the stressed environment for the breeding lines, compared to the landraces, suggesting that the evaluation of breeding materials under non-stressed conditions should be continued. Unlike the modern cultivar, the landraces were low yielding, and less responsive to non-stressed environments for grain yield and yield attributes. The drought resistance indices, i.e. tolerance index (TOL) and stress susceptibility index (SSI), were better in landraces than breeding lines, while the drought tolerance indices, i.e. stress tolerance index (STI) and drought response index (DRI), were better in breeding lines. In contrast with landraces, the modern cultivar and the breeding lines showed significant changes for both grain yield and drought tolerance.


Plant Disease ◽  
2013 ◽  
Vol 97 (5) ◽  
pp. 590-600 ◽  
Author(s):  
Richard W. Smiley ◽  
Juliet M. Marshall ◽  
Jennifer A. Gourlie ◽  
Timothy C. Paulitz ◽  
Shyam L. Kandel ◽  
...  

The cereal cyst nematode Heterodera avenae reduces wheat yields in the Pacific Northwest. Previous evaluations of cultivar resistance had been in controlled environments. Cultivar tolerance had not been evaluated. Seven spring wheat trials were conducted in naturally infested fields in three states over 2 years. A split-plot design was used for all trials. Five trials evaluated both tolerance and resistance in 1.8-by-9-m plots treated or not treated with nematicides. Two trials evaluated resistance in 1-m head rows where each wheat entry was paired with an adjacent row of a susceptible cultivar. Cultivars with the Cre1 resistance gene (‘Ouyen’ and ‘Chara’) reduced the postharvest density of H. avenae under field conditions, confirming Cre1 parents as useful for germplasm development. Ouyen was resistant but it was also intolerant, producing significantly lower grain yield in controls than in plots treated with nematicides. Susceptible cultivars varied in tolerance. Undefined resistance was identified in one commercial cultivar (‘WB-Rockland) and four breeding lines (UC1711, SO900163, SY-B041418, and SY-97621-05). This research was the first systematic field demonstration of potential benefits to be derived through development and deployment of cultivars with resistance plus tolerance to cereal cyst nematode in North America.


2017 ◽  
Author(s):  
Tak Lee ◽  
Sohyun Hwang ◽  
Chan Yeong Kim ◽  
Hongseok Shim ◽  
Hyojin Kim ◽  
...  

Gene networks provide a system-level overview of genetic organizations and enable the dissection of functional modules underlying complex traits. Here we report the generation of WheatNet, the first genome-scale functional network for T. aestivum and a companion web server (www.inetbio.org/wheatnet). WheatNet was constructed by integrating 20 distinct genomics datasets, including 156,000 wheat-specific co-expression links mined from 1,929 microarray data. A unique feature of WheatNet is that each network node represents either a single gene or a group of genes. We computationally partitioned gene groups mimicking homeologous genes by clustering 99,386 wheat genes, resulting in 20,248 gene groups comprising 63,401 genes and 35,985 individual genes. Thus, WheatNet was constructed using 56,233 nodes, and the final integrated network has 20,230 nodes and 567,000 edges. The edge information of the integrated WheatNet and all 20 component networks are available for download.


2021 ◽  
Author(s):  
Lance F. Merrick ◽  
Arron H. Carter

AbstractTraits with a complex unknown genetic architecture are common in breeding programs. However, they pose a challenge for selection due to a combination of complex environmental and pleiotropic effects that impede the ability to create mapping populations to characterize the trait’s genetic basis. One such trait, seedling emergence of wheat (Triticum aestivumL.) from deep planting, presents a unique opportunity to explore the best method to use and implement GS models to predict a complex trait. 17 GS models were compared using two training populations, consisting of 473 genotypes from a diverse association mapping panel (DP) phenotyped from 2015-2019 and the other training population consisting of 643 breeding lines phenotyped in 2015 and 2020 in Lind, WA with 40,368 markers. There were only a few significant differences between GS models, with support vector machines reaching the highest accuracy of 0.56 in a single breeding line trial using cross-validations. However, the consistent moderate accuracy of cBLUP and other parametric models indicates no need to implement computationally demanding non-parametric models for complex traits. There was an increase in accuracy using cross-validations from 0.40 to 0.41 and independent validations from 0.10 to 0.17 using diversity panels lines to breeding lines. The environmental effects of complex traits can be overcome by combining years of the same populations. Overall, our study showed that breeders can accurately predict and implement GS for a complex trait by using parametric models within their own breeding programs with increased accuracy as they combine training populations over the years.


HortScience ◽  
2020 ◽  
Vol 55 (7) ◽  
pp. 1132-1143
Author(s):  
Qirui Cui ◽  
Haizheng Xiong ◽  
Yufeng Yufeng ◽  
Stephen Eaton ◽  
Sora Imamura ◽  
...  

Cowpea [Vigna unguiculate (L.) Walp.] is not only a healthy, nutritious, and versatile leguminous crop; it also has a relatively high adaptation to drought. Research has shown that cowpea lines have a high tolerance to drought, and many of them can survive more than 40 days under scorching and dry conditions. The cowpea (Southern pea) breeding program at the University of Arkansas has been active for more than 50 years and has produced more than 1000 advanced breeding lines. The purpose of this study was to evaluate the drought-tolerant ability in Arkansas cowpea lines and use the drought-tolerant lines in cowpea production or as parents in cowpea breeding. A total of 36 University of Arkansas breeding lines were used to screen drought tolerance at the seedling stage in this study. The experiment was conducted in the greenhouse using a randomized complete block design (RCBD) with two replicates, organized in a split-plot manner, where the drought treatment (drought and nondrought stress) as the main plot and the cowpea genotypes as the subplot. Drought stress was applied for 4 weeks, and three drought-tolerant–related traits were collected and analyzed. Results showed that cowpea breeding lines: ‘17-61’, ‘17-86’, ‘Early Scarlet’, and ‘ARBlackeye #1’ were found to be drought tolerant.


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