Research Article: Genome-wide association analyses for yield and yield-related traits in bread wheat (Triticum aestivum L.) under pre-anthesis combined heat and drought stress in field conditions

Date Published: March 18, 2019

Publisher: Public Library of Science

Author(s): Mirza Faisal Qaseem, Rahmatullah Qureshi, Humaira Shaheen, Noshin Shafqat, Aimin Zhang.


Understanding the genetic basis of heat and drought stress tolerance in wheat is prerequisite for wheat breeding program. In the present study, a wheat panel comprising of 192 elite bread wheat genotypes was phenotyped in eight environments for yield and related traits in field conditions. Four stress environments were created by implying four different treatments differing in sowing date and water availability, panel was evaluated for two years in field conditions. The panel was genotyped with 15K Illumina chip and 9236 polymorphic markers concentrated on B genome were employed in GWAS analysis. Consistent, fast LD decay was observed on D genome and structure analysis germplasm divided panel into three major populations. GWAS was performed using BLUEs values of combined environment data in R package GAPIT using log10(P) = 3.96 as significance threshold. The significance of association was further checked using FDR<0.05 threshold. The GWAS identified 487 loci associated with the traits and were significant at log10(p) threshold out of these 350 loci were significant at FDR threshold. For two stress indices 108 associations were significant at FDR threshold. Nine genomic regions were shared among all treatment, while multiple pleiotropic regions were present on chromosome 7D followed by unmapped chromosome. The present study validated many marker trait associations for yield and other traits, MTAs significant under combined drought and heat stress were novel. These regions are important and can be used for fine mapping and marker assisted selection to discover new genes responsible for heat and drought tolerance in wheat.

Partial Text

Bread wheat is world’s 3rd most cultivated cereal crop planted over more than 20% area and provide 20% calories and 20% plant derived proteins to global population [1,2]. Global wheat demand is increasing with continuous increase in population and it is estimated that there is a need to increase global wheat production by 70% in 2050 [3]. Due to uncertainty in climatic conditions, it is estimated that wheat yield will reduce by 50% in South Asia in 2050 which is 7% of total global crop reduction [4]. This vulnerability in wheat yield is due to changes in patterns of rainfall, increase in temperature and occurrence of simultaneous drought and heat stress during the grain filling period. Increase in air temperature, radiation stress, high levels of CO2 and increase in the amount of greenhouse gasses further increase the intensity of drought and heat stress [5–7]. In coming few decade scenario of climate change will worsen, it is predicted that global temperature will increase by 3–5°C and annual precipitation will decrease by 4–27% in different parts of world [8]. The major adverse effects of heat stress on wheat include reduction in crop cycle, increase in soil temperature and rate of evaporation while drought stress mainly effects sink and source strength. Interactive effects of drought and heat stress may come from increased vapour pressure deficit. Many attempts have been made by using conventional breeding strategies to improve grain yield and quality of bread wheat, but these approaches altogether increased yield by less than one percent per year [9–12]. Future wheat breeding program is based on dissecting molecular and genetic basis of heat and drought stress tolerance through complementary approaches of association mapping and QTL mapping [13–15]. Till many years QTL mapping was considered as a powerful tool for genetic dissection of complex traits in plants but now QTL mapping is replaced by association mapping. Association mapping is based on linkage disequilibrium (LD) and is a powerful approach with higher resolution due to presence of higher genetic diversity and historic recombination of alleles among association mapping populations [16]. Association mapping is used to identify genomic regions associated with heat and drought tolerance in many association mapping populations [17–20] but these studies focus only either on heat or drought stress. Only few studies focused on combined drought and heat stress [21–24]. In the present study a diverse panel of bread wheat genotype was phenotyped under optimum [C], drought [D], heat [H] and combined heat and drought stressed [HD] conditions for two cropping years. In addition to assessing genetic diversity of the panel significant markers traits associations were identified for each stress treatment. Furthermore, common association among stress treatment and pleiotropic regions shared by multiple traits were also assessed.

The yield traits were recorded from all three plants per genotype while physiological data was recorded from three randomly selected plants. Following yield traits were recorded during study; awn length (AL) (from tip of spike), days to anthesis (DTA) (number of days taken from emergence to appearance of anthers), day to maturity (DTM) (number of days taken from emergence to maturity), grains per spike (GPS) (number of grains in spike was counted), grain yield (GY) (weighing grains form all harvested plants), harvest index (HI) (percent ratio of grain yield and above ground plant dry weight (DW), peduncle extrusion (PEXT) (from tip of flag leaf to base of spike), peduncle length (PL) (from first node to base of spike), plant height (PH) (from ground level to spike tip excluding awns), spikelet number (SLP) (counting number of fertile tillers), spike length (SL) (manually with ruler in cm). Stress tolerance index (STI) Tolerance index (TOL)
where Ys and Yp represent yield under stress and non-stress treatment and Yp2 is the mean yield of wheat lines evaluated under non-stress conditions [25].

In last few decades lots of efforts had been made to study the effects of a single stress on plants under control and field conditions [36]. However, in open field conditions, plant have to face multiple biotic and abiotic stresses at same time and one cannot really understand the effects of these combined stresses by applying one stress separately in controlled lab conditions. The combination of two or more stresses alters plant proteomics, metabolism and genetics in a unique way which is totally different from changes imposed by individual stress [23,37,38]. To address this scenario, we aimed to determine independent and combined effect of drought and heat stress on wheat yield and related traits and finding out genomic regions associated with heat and drought stress tolerance.

The identification and introgression of major-effect QTLs are one of the best and proven approaches to improving the stress tolerance of wheat varieties. The accuracy and consistency of QTLs have clearly shown that structured association mapping with genome-wide molecular markers is an attractive option to identify major-effect QTLs for GY under different stress treatments. Association mapping results revealed many novel regions associated with combined drought and heat stress tolerance, along with nine consistent regions common among all four treatments and many pleiotropic regions associated with more than one traits. Further exploration of common regions among treatments through marker assisted selection can help in understanding complex mechanisms of abiotic stress tolerance and fine mapping of these regions can lead to new gene discoveries. Intensity of climate change will increase in next few years and will decrease wheat production, thus it is need of time to improve germplasm by arranging crosses between diverse parents and improve genomic technology and couple these technologies with marker assisted selection. The present study will help in understanding irrigation use efficiency and tolerance of exotic lines to rain fed conditions. It will help in identification and inclusion of tolerant genotypes in breeding program for further strengthening.




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