Multienvironment QTL analysis delineates a major locus associated with homoeologous exchanges for water‐use efficiency and seed yield in canola. (5th May 2022)

• Record Type: Journal Article
• Authors: Raman, Harsh; Raman, Rosy; Pirathiban, Ramethaa; McVittie, Brett; Sharma, Niharika; Liu, Shengyi; Qiu, Yu; Zhu, Anyu; Kilian, Andrzej; Cullis, Brian; Farquhar, Graham D.; Stuart‐Williams, Hilary; White, Rosemary; Tabah, David; Easton, Andrew; Zhang, Yuanyuan
• Is Part Of: Plant, cell and environment. Volume 45:Number 7(2022)
• Page Start: 2019
• Page End: 2036
• Publication Date: 2022-05-05
• Subjects: carbon isotope discrimination -- drought avoidance -- gene expression -- genetic analysis -- physiology -- water use; Plant physiology -- Periodicals; Plant cells and tissues -- Periodicals; Plant communities -- Periodicals; 581.105
• DOI: 10.1111/pce.14337
• Languages: English
• ISSNs: 0140-7791

Abstract

Abstract: Canola varieties exhibit variation in drought avoidance and drought escape traits, reflecting adaptation to water‐deficit environments. Our understanding of underlying genes and their interaction across environments in improving crop productivity is limited. A doubled haploid population was analysed to identify quantitative trait loci (QTL) associated with water‐use efficiency (WUE) related traits. High WUE in the vegetative phase was associated with low seed yield. Based on the resequenced parental genome data, we developed sequence‐capture‐based markers and validated their linkage with carbon isotope discrimination (Δ 13 C) in an F2 population. RNA sequencing was performed to determine the expression of candidate genes underlying Δ 13 C QTL. QTL contributing to main and QTL × environment interaction effects for Δ 13 C and yield were identified. One multiple‐trait QTL for Δ 13 C, days to flower, plant height, and seed yield was identified on chromosome A09. Interestingly, this QTL region overlapped with a homoeologous exchange (HE) event, suggesting its association with the multiple traits. Transcriptome analysis revealed 121 significantly differentially expressed genes underlying Δ 13 C QTL on A09 and C09, including in HE regions. Sorting out the negative relationship between vegetative WUE and seed yield is a priority. Genetic and genomic resources and knowledge so developed could improve canola WUE and yield. Summary Statement: Growing concerns about reduced water availability and climate change are putting pressure on sustainable food production worldwide. Identification of varieties, suitable for cultivation under reduced water inputs is critical to developing resilience to drought conditions. We identified 29 genetic and environmental determinants underlying plasticity in water use efficiency (WUE) and productivity traits. We show that one of the quantitative trait loci underlying variation in Δ 13 C, flowering time, plant height, and seed yield is subjected to homoeologous exchange and causes dosage‐dependent gene expression changes in WUE. Our results provide insights into the complexity of WUE genes and provide a strategy for improving canola adaptation under water‐deficit conditions.