Siddiqui, Md. Nurealam: Genetic variations in root architecture traits for water and nitrogen use efficiency in wheat and barley. - Bonn, 2022. - Dissertation, Rheinische Friedrich-Wilhelms-Universität Bonn.
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author = {{Md. Nurealam Siddiqui}},
title = {Genetic variations in root architecture traits for water and nitrogen use efficiency in wheat and barley},
school = {Rheinische Friedrich-Wilhelms-Universität Bonn},
year = 2022,
month = nov,

note = {The soil edaphic resources such as water and nitrogen are essential for crop production because they are required by plants for proper growth and tissue development. The global crop production is vulnerable due to rapid climatic changes and scarcity of natural resources. Insufficient water availability in the soil swiftly translates to water deficiency in plant systems, which in turn affects metabolism and developmental processes, ultimately arresting plant growth and yield stability. Yield reduction caused by drought typically ranges between 30 to 90% in the field. In the majority of agricultural regions, nitrogen (N) availability is the most limiting factor for crop production. However, excess N fertilization affects soil acidification processes, thereby reducing soil fertility. Additionally, rapid pollution of ground and surface water is caused by nitrate leaching, a direct consequence of excess/inadequate N fertilization. This may affect biodiversity and promotes harmful climatic changes as well as reduced air quality. Therefore, developing cultivars with high water and nitrogen use efficiency (WUE and NUE) is crucial for economic cereal production and the protection of ecosystems.
The root is the foremost plant organ responsible for extracting soil resources in water- and nutrient-limited conditions. When plants sense a water shortage, roots continue to grow into deep soil layers to facilitate the uptake of available water and nutrients. To this end, identifying genetic factors and candidate genes affecting root architecture and characterizing their roles in adaptation to water and N deficiency should be addressed. Therefore, this thesis employs genetic and molecular approaches to explore natural variations in root phenotype, anatomy and transcriptomic profiles to study the underlying genetic architecture of candidate genes associated with WUE and NUE.
To decipher the genetic control mechanisms for root phenotypic adaptation to water availability, root system architecture traits of a diverse set of 200 winter wheat genotypes, grown with and without water in the field, were evaluated. Water stress differentially modulated root architecture and plasticity traits. A total of 25 marker-trait associations connected to natural variations in root architecture and plasticity were identified by GWAS. They were distributed on chromosomes 1A, 1B, 2A, 2B, 3A, 3B, 4B, 5A, 5D, 7A and 7B. In total, 396 putative candidate genes associated with root plasticity were detected using linkage disequilibrium analysis. Interestingly, these genes were directly involved in water transport and channel activity, cellular response to water deprivation, scavenging reactive oxygen species, root growth and development as well as hormone-activated signaling pathway-transmembrane transport; biological processes essential to regulate WUE. Transcript expression analysis revealed that the candidate genes were highly expressed in roots at multiple root growth stages and during drought treatments. We found that traits affecting root phenotypic plasticity were highly quantitative, and the associated loci were involved in WUE pathways.
Next, we were curious how root architecture traits contribute to NUE by regulating nitrate transport systems in wheat and barley. To achieve this, we performed a comparative genome-wide scan using wheat and barley datasets characterized under high and low N input. We identified several candidate genes involved in NUE, including NPF2.12, a convergently selected low-affinity nitrate transporter gene. Phylogenetic analysis revealed that NPF2.12 encodes a highly convergent MAJOR FACILITATOR SUPERFAMILY domain-containing protein with nitrate transporter activity. In response to low nitrate availability, we observed that variations in the NPF2.12 promoter resulted in higher root growth and root-to-shoot nitrate transport by decreasing its transcript expression in both wheat and barley. Further, a loss-of-function npf2.12 allele transactivated NIA1, a gene encoding for a nitrate reductase, that enhanced nitric oxide production under low nitrate conditions and led to competent root growth and nitrate transport comparable to the wild-type. Importantly, multiple field trials showed that the TaNPF2.12TT allele significantly enhanced N uptake, N transport in leaves and grains and subsequently NUE under low N supply. Thus, we identified NPF2.12 as a convergently selected nitrate transporter and an NPF2.12-NIA1 signaling cascade that can be exploited to improve NUE or rather root growth at low N availability.
In summary, this thesis provides genetic and molecular mechanisms underlying root architectural adaptation to water- and N-deficit conditions. The identified root architecture traits, syntenic loci and transporter genes can be targeted in breeding programs for high-resolution gene trait analyses to develop cultivars with improved WUE and NUE.},

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