Finding genomic regions and candidate genes governing water use efficiency in rice

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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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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Integrating genome annotation and QTL position to identify candidate genes for productivity, architecture and water-use efficiency in Populus spp

BMC Plant Biology ◽

10.1186/1471-2229-12-173 ◽

2012 ◽

Vol 12 (1) ◽

pp. 173 ◽

Cited By ~ 30

Author(s):

Romain Monclus ◽

Jean-Charles Leplé ◽

Catherine Bastien ◽

Pierre-François Bert ◽

Marc Villar ◽

...

Keyword(s):

Water Use Efficiency ◽

Candidate Genes ◽

Water Use ◽

Genome Annotation ◽

Use Efficiency ◽

Populus Spp

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Growth, gas exchange and water use efficiency of the facultative hemiparasite Rhinanthus minor associated with hosts differing in foliar nitrogen concentration

Physiologia Plantarum ◽

10.1034/j.1399-3054.1993.890110.x ◽

1993 ◽

Vol 89 (1) ◽

pp. 64-70 ◽

Cited By ~ 13

Author(s):

W.E. Seel ◽

R.E. Cooper ◽

M.C. Press

Keyword(s):

Gas Exchange ◽

Water Use Efficiency ◽

Water Use ◽

Nitrogen Concentration ◽

Foliar Nitrogen ◽

Use Efficiency ◽

Rhinanthus Minor

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Increasing intrinsic water-use efficiency over the past 160 years does not stimulate tree growth in southeastern China

Climate Research ◽

10.3354/cr01526 ◽

2018 ◽

Vol 76 (2) ◽

pp. 115-130 ◽

Cited By ~ 5

Author(s):

G Guo ◽

K Fang ◽

J Li ◽

HW Linderholm ◽

D Li ◽

...

Keyword(s):

Water Use Efficiency ◽

Water Use ◽

Tree Growth ◽

Southeastern China ◽

The Past ◽

Intrinsic Water Use Efficiency ◽

Use Efficiency

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A comparative appraisal of urea super granule application in raised bed and prilled urea application in conventional planting for transplanted boro rice (Oryza sativa)

JOURNAL OF ADVANCES IN AGRICULTURE ◽

10.24297/jaa.v6i1.5388 ◽

2016 ◽

Vol 6 (1) ◽

pp. 822-832

Author(s):

Halim Mahmud Bhuyan ◽

Most. Razina Ferdousi ◽

Mohammad Toufiq Iqbal ◽

Ahmed Khairul Hasan

Keyword(s):

Water Use Efficiency ◽

Water Use ◽

N Fertilizer ◽

Deep Placement ◽

Prilled Urea ◽

Planting Methods ◽

Weed Infestation ◽

Use Efficiency ◽

Raised Bed ◽

Boro Rice

Utilization of urea super granule (USG) with raised bed cultivation system for transplanted boro (winter, irrigated) rice production is a major concern now days. A field experiment was conducted in the chuadanga district of Bangladesh to compare the two cultivation methods: deep placement of USG on raised bed with boro rice, and prilled urea (PU) broadcasting in conventional planting. Results showed that USG in raised bed planting increased grain yields of transplanted boro rice by up to 18.18% over PU in conventional planting. Deep placement of USG in raised bed planting increased the number of panicle m-2, number of grains panicle-1 and 1000-grains weight of boro rice than the PU in conventional planting. Better plant growth was observed by deep placement of USG in raised bed planting compared to PU in conventional planting. Sterility percentage and weed infestation were lower on USG in raised bed planting compared to the PU in conventional planting methods. Forty seven percent irrigation water and application time could be saved by USG in raised bed planting than PU in conventional planting. Deep placement of USG in bed saved N fertilizer consumption over conventional planting. Water use efficiency for grain and biomass production was higher with deep placement of USG in bed planting than the PU broadcasting in conventional planting methods. Similarly, agronomic efficiency of N fertilizer by USG in bed planting was significantly higher than the PU broadcasting in conventional planting. This study concluded that deep placement of USG in raised bed planting for transplanted boro rice is a new approach to achieve fertilizer and water use efficiency as well as higher yield and less water input compared to existing agronomic practices in Bangladesh.

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