Muhammad Imtiaz

Genome-wide association for grain yield under rainfed conditions in historical wheat cultivars from Pakistan

Genome-wide association studies (GWAS) were undertaken to identify SNP markers associated with yield and yield-related traits in 123 Pakistani historical wheat cultivars evaluated during 2011-2014 seasons under rainfed field conditions. The population was genotyped by using high-density Illumina iSelect 90K single nucleotide polymorphism (SNP) assay, and finally 14,960 high quality SNPs were used in GWAS. Population structure examined using 1000 unlinked markers identified seven subpopulations (K = 7) that were representative of different breeding programs in Pakistan, in addition to local landraces. Forty four stable marker-trait associations (MTAs) with -log p > 4 were identified for nine yield-related traits. Nine multi-trait MTAs were found on chromosomes 1AL, 1BS, 2AL, 2BS, 2BL, 4BL, 5BL, 6AL, and 6BL, and those on 5BL and 6AL were stable across two seasons. Gene annotation and syntey identified that 14 trait-associated SNPs were linked to genes having significant importance in plant development. Favorable alleles for days to heading (DH), plant height (PH), thousand grain weight (TGW), and grain yield (GY) showed minor additive effects and their frequencies were slightly higher in cultivars released after 2000. However, no selection pressure on any favorable allele was identified. These genomic regions identified have historically contributed to achieve yield gains from 2.63 million tons in 1947 to 25.7 million tons in 2015. Future breeding strategies can be devised to initiate marker assisted breeding to accumulate these favorable alleles of SNPs associated with yield-related traits to increase grain yield. Additionally, in silico identification of 454-contigs corresponding to MTAs will facilitate fine mapping and subsequent cloning of candidate genes and functional marker development.

Markers Linked to Wheat Stem Rust Resistance Gene Sr11 Effective to Puccinia graminis f. sp. tritici Race TKTTF.

Wheat stem rust, caused by Puccinia graminis f. sp. tritici, can cause severe yield losses on susceptible wheat varieties and cultivars. Although stem rust can be controlled by the use of genetic resistance, population dynamics of P. graminis f. sp. tritici can frequently lead to defeat of wheat stem rust resistance genes. P. graminis f. sp. tritici race TKTTF caused a severe epidemic in Ethiopia on Ug99-resistant Digalu in 2013 and 2014. The gene Sr11 confers resistance to race TKTTF and is present in Gabo 56. We identified seven single-nucleotide polymorphism (SNP) markers linked to Sr11 from a cross between Gabo 56 and Chinese Spring exploiting a 90K Infinium iSelect Custom beadchip. Five SNP markers were validated on a Berkut/Scalavatis population that segregated for Sr11, using KBioscience competitive allele-specific polymerase chain reaction (KASP) assays. Two of the SNP markers, KASP_6BL_IWB10724 and KASP_6BL_IWB72471, were predictive of Sr11 among wheat genetic stocks, cultivars, and breeding lines from North America, Ethiopia, and Pakistan. These markers can be utilized to select for Sr11 in wheat breeding and to detect the presence of Sr11 in uncharacterized germplasm.

Strategic crossing of biomass and harvest index—source and sink—achieves genetic gains in wheat

To accelerate genetic gains in breeding, physiological trait (PT) characterization of candidate parents can help make more strategic crosses, increasing the probability of accumulating favorable alleles compared to crossing relatively uncharacterized lines. In this study, crosses were designed to complement “source” with “sink” traits, where at least one parent was selected for favorable expression of biomass and/or radiation use efficiency—source—and the other for sink-related traits like harvest-index, kernel weight and grains per spike. Female parents were selected from among genetic resources—including landraces and products of wide-crossing (i.e. synthetic wheat)—that had been evaluated in Mexico at high yield potential or under heat stress, while elite lines were used as males. Progeny of crosses were advanced to the F4 generation within Mexico, and F4-derived F5 and F6 generations were yield tested to populate four international nurseries, targeted to high yield environments (2nd and 3rd WYCYT) for yield potential, and heat stressed environments (2nd and 4th SATYN) for climate resilience, respectively. Each nursery was grown as multi-location yield trials. Genetic gains were achieved in both temperate and hot environments, with most new PT-derived lines expressing superior yield and biomass compared to local checks at almost all international sites. Furthermore, the tendency across all four nurseries indicated either the superiority of the best new PT lines compared with the CIMMYT elite checks, or the superiority of all new PT lines as a group compared with all checks, and in some cases, both. Results support—in a realistic breeding context—the hypothesis that yield and radiation use efficiency can be increased by improving source:sink balance, and validate the feasibility of incorporating exotic germplasm into mainstream breeding efforts to accelerate genetic gains for yield potential and climate resilience.

Acceptance and competitiveness of new improved wheat varieties by smallholder farmers

ABSTRACT We conducted this research because earlier research revealed that Pakistani farmers were growing 8–10-year-old wheat (Triticum aestivum L.) varieties and hence not benefitting from the recent advances in wheat breeding. Participatory varietal selection (PVS) trials were conducted to have farmers validate and include newly released wheat varieties into seed-production stream to speed up replacement of old and obsolete wheat varieties by farmer-preferred new high-yielding varieties. Fourteen new varieties recommended for irrigated and eight for rainfed environments were evaluated in this research involving smallholder farmers in food-deficit districts of Pakistan. Collaborating farmers preferred 10 varieties from the PVS trials, eight of which were germplasm from the International Maize and Wheat Improvement Center (CIMMYT) that yielded on average 5–17% more grain than local checks. Local checks used in the PVS trials in Sindh and Khyber Pakhtunkhwa were old improved varieties. Greater yield advantage from new varieties over local checks was reported from rainfed environments and areas where old local checks were used. The PVS research showed the possibility of ensuring food security of smallholder farmers as new high-yielding varieties gave an additional 0.3 –0.5 tons of grain per ha, sufficient to feed two to three persons per year. Research also revealed that innovative farmers in rainfed regions grew wheat varieties recommended for irrigated regions to identify high-yielding wheat varieties with stable performance. Feedback by farmers to wheat breeding research system was to develop even higher yielding new wheat varieties with diseases resistance to replace old and obsolete varieties to boost food security.

Harnessing genetic potential of wheat germplasm banks through impact-oriented-prebreeding for future food and nutritional security

The value of exotic wheat genetic resources for accelerating grain yield gains is largely unproven and unrealized. We used next-generation sequencing, together with multi-environment phenotyping, to study the contribution of exotic genomes to 984 three-way-cross-derived (exotic/elite1//elite2) pre-breeding lines (PBLs). Genomic characterization of these lines with haplotype map-based and SNP marker approaches revealed exotic specific imprints of 16.1 to 25.1%, which compares to theoretical expectation of 25%. A rare and favorable haplotype (GT) with 0.4% frequency in gene bank identified on chromosome 6D minimized grain yield (GY) loss under heat stress without GY penalty under irrigated conditions. More specifically, the ‘T’ allele of the haplotype GT originated in Aegilops tauschii and was absent in all elite lines used in study. In silico analysis of the SNP showed hits with a candidate gene coding for isoflavone reductase IRL-like protein in Ae. tauschii. Rare haplotypes were also identified on chromosomes 1A, 6A and 2B effective against abiotic/biotic stresses. Results demonstrate positive contributions of exotic germplasm to PBLs derived from crosses of exotics with CIMMYT’s best elite lines. This is a major impact-oriented pre-breeding effort at CIMMYT, resulting in large-scale development of PBLs for deployment in breeding programs addressing food security under climate change scenarios.

Correction to: Strategic crossing of biomass and harvest index—source and sink—achieves genetic gains in wheat

The original article was corrected. Author Muhammad Kundi should instead read: Muhammad Sohail.

Implications of less tail end water on livelihoods of small farmers in Pakistan

In Pakistan, about 80% of the cropped area is irrigated using canal irrigation, and water availability is closely linked to the location of the farm. Using data collected from 950 farmers through a field survey covering four provinces (Punjab, Sindh, Khyber Pakhtunkhwa and Balochistan), this study aimed to assess the impact of location, that is, ‘head’ versus ‘tail’ on water availability and its impact on crop yield, household income, food security and poverty levels. The censored least absolute deviation was used to estimate farmer participation in water markets, and the propensity score matching was used to assess impacts on yield of wheat and rice, household income and poverty levels as well as land rent and water scarcity. The results show that farmers situated at the head of the water source have higher wheat and rice yields in the range of 2–3 maunds per acre. Household income levels are higher in the range of PKR 8455–14,673, and poverty levels are lower (+3% to 5%). The land rent at the head is higher compared to the tail while water scarcity is also less at the head. The study indicated that farmers’ status plays a major role in land location and access to irrigation water.

Effects of Temperature Stresses on the Resistance of Chickpea Genotypes and Aggressiveness of Didymella rabiei Isolates

Chickpea (Cicer arietinum L.) is an important food and rotation crop in many parts of the world. Cold (freezing and chilling temperatures) and Ascochyta blight (Didymella rabiei) are the major constraints in chickpea production. The effects of temperature stresses on chickpea susceptibility and pathogen aggressiveness are not well documented in the Cicer-Didymella pathosystem. Two experiments were conducted under controlled conditions using chickpea genotypes and pathogen isolates in 2011 and 2012. In Experiment 1, four isolates of D. rabiei (AR-01, AR-02, AR-03 and AR-04), six chickpea genotypes (Ghab-1, Ghab-2, Ghab-3, Ghab-4, Ghab-5 and ICC-12004) and four temperature regimes (10, 15, 20, and 25°C) were studied using 10 day-old seedlings. In Experiment 2, three chickpea genotypes (Ghab-1, Ghab-2, and ICC-12004) were exposed to 5 and 10 days of chilling temperature exposure at 5°C and non-exposed seedlings were used as controls. Seedlings of the three chickpea genotypes were inoculated with the four pathogen isolates used in Experiment 1. Three disease parameters (incubation period, latent period and disease severity) were measured to evaluate treatment effects. In Experiment 1, highly significant interactions between genotypes and isolates; genotypes and temperature; and isolate and temperature were observed for incubation and latent periods. Genotype x isolate and temperature x isolate interactions also significantly affected disease severity. The resistant genotype ICC-12004 showed long incubation and latent periods and low disease severity at all temperatures. The highly aggressive isolate AR-04 caused symptoms, produced pycnidia in short duration as well as high disease severity across temperature regimes, which indicated it is adapted to a wide range of temperatures. Short incubation and latent periods and high disease severity were observed on genotypes exposed to chilling temperature. Our findings showed that the significant interactions of genotypes and isolates with temperature did not cause changes in the rank orders of the resistance of chickpea genotypes and aggressiveness of pathogen isolates. Moreover, chilling temperature predisposed chickpea genotypes to D. rabiei infection; developing multiple stress resistance is thus a pre-requisite for the expansion of winter-sown chickpea in West Asia and North Africa.

Yield and Profit from New and Old Wheat Varieties Using Certified and Farmer-Saved Seeds

Wheat is a strategic crop for food security in Pakistan with predominance of smallholder farmers. Farmer-saved seed (FSS) is used nearly by 75% of farmers for wheat production. Frequent variety or seed replacement is uncommon even among large-scale farmers, and certified seed (CS) is mostly bought to verify the value of new varieties. Replacing old and obsolete varieties by new high yielding disease resistant varieties is key to transferring new genetic gains to farmers. For the first time in Pakistan, on-farm factorial experiments involving seven new and five old wheat varieties and their corresponding CS and FSS were conducted. A total of 49 farmers representing major wheat cropping patterns throughout the country participated in these trials in the 2014 and 2015 wheat growing seasons. Analysis of variance revealed that there was highly significant difference between wheat varieties and between seed classes. New variety + CS gave 33.8% more grain yield as well as higher marginal return over farmers’ variety + FSS. Grain yield and returns from new variety + FSS and farmers’ variety + CS were at par. Scientific knowledge generated in this research demonstrated that use of CS of new wheat varieties is best option, while growing new varieties with FSS is a second choice for the advantages accruing from their built-in genetic traits of economic importance over growing CS of old and obsolete varieties. Having more flexible seed system will help accelerate the delivery of new genetic gains to farmers’ fields.

Acceptability of GM foods among Pakistani consumers

In Pakistan majority of the consumers do not have information about genetically modified (GM) foods. In developing countries particularly in Pakistan few studies have focused on consumers acceptability about GM foods. Using comprehensive primary dataset collected from 320 consumers in 2013 from Pakistan, this study analyzes the determinants of consumers acceptability of GM foods. The data was analyzed by employing the bivariate probit model and censored least absolute deviation (CLAD) models. The empirical results indicated that urban consumers are more aware of GM foods compared to rural consumers. The acceptance of GM foods was more among females consumers as compared to male consumers. In addition, the older consumers were more willing to accept GM food compared to young consumers. The acceptability of GM foods was also higher among wealthier households. Low price is the key factor leading to the acceptability of GM foods. The acceptability of the GM foods also reduces the risks among Pakistani consumers.