Genes, haplotypes and physiological traits associated with a chromosome 3B locus for wheat improvement in hot climates

Abstract

Crop productivity in many wheat cultivation areas is severely affected by dry and hot conditions, increasing the yield gap between potential and actual yield. To close this gap, the identification of genes contributing to yield in stressed conditions is one key to the breeding of tolerant cultivars. However, due to low stability across environments, no genes have yet been identified for yield variation. In this project, we focussed on the positional cloning of a quantitative trait locus (QTL), qYDH.3BL, located on the wheat chromosome arm 3BL. The QTL has been identified by the multi-environment analysis of the double-haploid (DH) population of the cross from the drought tolerant line RAC875 and the susceptible variety Kukri. The QTL was constitutively expressed in the Mexican environment with the positive allele from RAC875 associated with an increase in yield, thousand grain weight and early vigour under dry and hot conditions. Greater allele effect dependent on temperature has been observed at qYDH.3BL, suggesting that the QTL is heat related. To fine map qYDH.3BL, we developed a deep-soil platform using 1 m deep wheelie bins placed in the polytunnel to increase temperature. We confirmed the expression of qYDH.3BL using a set of RAC875 x Kukri RILs. Single marker analysis showed the positive allele from RAC875 associated with spike length and biomass, early vigour and stem biomass. The development of a high-density genetic map of qYDH.3BL in RAC875, combined with the deep-platform experiment, narrowed the QTL interval to a 690 kbp sequence. The anchoring of the interval in the physical assembly of the wheat cv. Chinese Spring reference genome (IWGSC Ref 1.0) identified 12 candidate genes. The study of the allelic diversity at qYDH.3BL in a wheat diversity panel of 808 accessions identified four haplotypes. Haplotype I, the RAC875 allele was over-represented in the CIMMYT germplasm suggesting that the allele may have been selected for yield in a Mexican environment-type. To study the physiological mechanisms under qYDH.3BL control, we developed heterozygous inbred families (HIF). The lines were phenotyped in the deep soil platform. The lines with the RAC875 allele among the HIFs increased biomass, single grain weight and number of spikelets per spike. Water use was also measured in the deep soil platform using sap flow sensors. RAC875 had an increased water use compared to Kukri. A similar pattern was observed in the HIFs, the lines with the RAC875 allele had a higher water use compared to those with the Kukri allele. As qYDH.3BL was constitutively expressed in the Mexican environments characterised by a deep soil and RAC875 was shown to have a lower root conductivity than Kukri due to its root anatomy, we also phenotyped the roots of the HIFs. We did not identify root traits that could contribute to the heat tolerance mechanism associated with qYDH.3BL. Finally, we studied the expression of the 12 candidate genes within the 690 kbp interval in the HIFs. Expression analysis identified a strong candidate gene, Seven in absentia (TaSINA). The gene was up-regulated in Kukri compared to RAC875 and in the HIFs containing the Kukri allele compared to those with the RAC875 allele. TaSINA is annotated as an E3 ubiquitin ligase protein, a family involved in ubiquitin pathway. To study the role of TaSINA in drought and heat tolerance, we screened the Gladius TILLING population and identified two missense variants. Study of the phylogenetic relationship of TaSINA with published SINA genes in plants and animals revealed that TaSINA is specific to the Triticeae. This is the first report of a wheat SINA gene and a gene associated to yield variation under heat in wheat. Discovery of new alleles of TaSINA could lead to the breeding of new varieties able to maintain yield under heat stress conditions.