Molecular and genetic basis of plant macronutrient use efficiency: concepts, opportunities, and challenges

Stomata allow CO2 uptake by leaves for photosynthetic assimilation at the cost of water vapor loss to the atmosphere. The opening and closing of stomata in response to fluctuations in light intensity regulate CO2 and water fluxes and are essential to maintenance of water-use efficiency (WUE). However, little is known about the genetic basis for natural variation in stomatal movement, especially in C4 crops. This is partly because the stomatal response to a change in light intensity is difficult to measure at the scale required for association studies. High-throughput thermal imaging was used to bypass the phenotyping bottleneck and assess 10 traits describing stomatal conductance (gs) before, during and after a stepwise decrease in light intensity for a diversity panel of 659 sorghum accessions. Results from thermal imaging significantly correlated with photosynthetic gas-exchange measurements. gs traits varied substantially across the population and were moderately heritable (h2 up to 0.72). An integrated genome-wide and transcriptome-wide association study (GWAS/TWAS) identified candidate genes putatively driving variation in stomatal conductance traits. Of the 239 unique candidate genes identified with greatest confidence, 77 were orthologs of Arabidopsis genes related to functions implicated in WUE, including stomatal opening/closing (24 genes), stomatal/epidermal cell development (35 genes), leaf/vasculature development (12 genes), or chlorophyll metabolism/photosynthesis (8 genes). These findings demonstrate an approach to finding genotype-to-phenotype relationships for a challenging trait as well as candidate genes for further investigation of the genetic basis of WUE in a model C4 grass for bioenergy, food, and forage production.

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Elucidating the genetic basis of biomass accumulation and radiation use efficiency in spring wheat and its role in yield potential

10.1101/465682 ◽

2018 ◽

Author(s):

Gemma Molero ◽

Ryan Joynson ◽

Francisco J. Pinera-Chavez ◽

Laura-Jayne Gardiner ◽

Carolina Rivera-Amado ◽

...

Keyword(s):

Spring Wheat ◽

Genetic Basis ◽

Genome Wide Association Study ◽

Biomass Accumulation ◽

Snp Markers ◽

Radiation Use Efficiency ◽

Yield Potential ◽

Growth Stages ◽

Use Efficiency ◽

Radiation Use

SummaryOne of the major challenges for plant scientists is increasing wheat (Triticum aestivum) yield potential (YP). A significant bottleneck for increasing YP is achieving increased biomass through optimization of Radiation Use Efficiency (RUE) along the crop cycle. Exotic material such as landraces and synthetic wheat has been incorporated into breeding programs in an attempt to alleviate this, however their contribution to YP is still unclear. To understand the genetic basis of biomass accumulation and RUE we applied genome-wide association study (GWAS) to a panel of 150 elite spring wheat genotypes including many landrace and synthetically derived lines. The panel was evaluated for 31traits over two years under optimal growing conditions and genotyped using the 35K Wheat Breeders array. Marker-trait-association identified 94 SNPs significantly associated with yield, agronomic and phenology related traits along with RUE and biomass at various growth stages that explained 7–17 % of phenotypic variation. Common SNP markers were identified for grain yield, final biomass and RUE on chromosomes 5A and 7A. Additionally we show that landrace and synthetic derivative lines showed higher thousand grain weight (TGW), biomass and RUE but lower grain number (GNO) and harvest index (HI). Our work demonstrates the use of exotic material as a valuable resource to increase YP. It also provides markers for use in marker assisted breeding to systematically increase biomass, RUE and TGW and avoid the TGW/GNO and BM/HI trade-off. Thus, achieving greater genetic gains in elite germplasm while also highlighting genomic regions and candidate genes for further study.

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Genetic basis of nitrogen use efficiency and yield stability across environments in winter rapeseed

BMC Genetics ◽

10.1186/s12863-016-0432-z ◽

2016 ◽

Vol 17 (1) ◽

Cited By ~ 14

Author(s):

Anne-Sophie Bouchet ◽

Anne Laperche ◽

Christine Bissuel-Belaygue ◽

Cécile Baron ◽

Jérôme Morice ◽

...

Keyword(s):

Nitrogen Use Efficiency ◽

Genetic Basis ◽

Yield Stability ◽

Nitrogen Use ◽

Use Efficiency ◽

Winter Rapeseed

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The genetic basis of water‐use efficiency and yield in lettuce

BMC Plant Biology ◽

10.1186/s12870-021-02987-7 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Annabelle Damerum ◽

Hazel K. Smith ◽

GJJ Clarkson ◽

Maria José Truco ◽

Richard W. Michelmore ◽

...

Keyword(s):

Stomatal Conductance ◽

Water Supply ◽

Water Use Efficiency ◽

Carbon Isotope ◽

Water Use ◽

Genetic Basis ◽

Carbon Isotope Discrimination ◽

Promising Candidate ◽

Use Efficiency ◽

Genomic Regions

Abstract Background Water supply limits agricultural productivity of many crops including lettuce. Identifying cultivars within crop species that can maintain productivity with reduced water supply is a significant challenge, but central to developing resilient crops for future water-limited climates. We investigated traits known to be related to water-use efficiency (WUE) and yield in lettuce, a globally important leafy salad crop, in a recombinant inbred line (RIL) lettuce mapping population, produced from a cross between the cultivated Lactuca sativa L. cv. Salinas and its wild progenitor L. serriola L. Results Wild and cultivated lettuce differed in their WUE and we observed transgressive segregation in yield and water-use traits in the RILs. Quantitative trait loci (QTL) analysis identified genomic regions controlling these traits under well-watered and droughted conditions. QTL were detected for carbon isotope discrimination, transpiration, stomatal conductance, leaf temperature and yield, controlling 4–23 % of the phenotypic variation. A QTL hotspot was identified on chromosome 8 that controlled carbon isotope discrimination, stomatal conductance and yield under drought. Several promising candidate genes in this region were associated with WUE, including aquaporins, late embryogenesis abundant proteins, an abscisic acid-responsive element binding protein and glutathione S-transferases involved in redox homeostasis following drought stress were also identified. Conclusions For the first time, we have characterised the genetic basis of WUE of lettuce, a commercially important and water demanding crop. We have identified promising candidate genomic regions determining WUE and yield under well-watered and water-limiting conditions, providing important pre-breeding data for future lettuce selection and breeding where water productivity will be a key target.

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