Genetic Mapping of Quantitative Trait Loci for Grain Yield under Drought in Rice under Controlled Greenhouse Conditions

Abstract

Drought stress is a constant threat to rice production worldwide. Most modern rice cultivars are sensitive to drought, and the effect is severe at the reproductive stage. Conventional breeding for drought resistant (DR) rice varieties is slow and limited due to the quantitative nature of the DR traits. Identification of genes (QTLs)/markers associated with DR traits is a prerequisite for marker-assisted breeding. Grain yield is the most important trait and to this end drought yield QTLs have been identified under field conditions. The present study reports identification of drought yield QTLs under controlled conditions without confounding effects of other factors prevalent under natural conditions. A linkage map covering 1,781.5 cM with an average resolution of 9.76 cM was constructed using an F2 population from a cross between two Japonica cultivars, Cocodrie (drought sensitive) and Vandana (drought tolerant) with 213 markers distributed over 12 rice chromosomes. A subset of 59 markers (22 genic SSRs and 37 SNPs) derived from the transcriptome of the parents were also placed in the map. Single marker analysis using 187 F2 : 3 progeny identified 6 markers distributed on chromosomes 1, 5, and 8 to be associated with grain yield under drought (GYD). Composite interval mapping identified six genomic regions/quantitative trait loci (QTL) on chromosome 1, 5, 8, and 9 to be associated with GYD. QTLs located on chromosome 1 (qGYD1.2, qGYD1.3), chromosome 5 (qGYD5.1) and chromosome 8 (qGYD8.1) were contributed by Vandana alleles, whereas the QTLs, qGYD1.1 and qQYD9.1 were contributed by Cocodrie alelles. The additive positive phenotypic variance explained by the QTLs ranged from 30.0 to 34.0%. Candidate genes annotation within QTLs suggested the role of transcription factors and genes involved in osmotic potential regulation through catalytic/metabolic pathways in drought tolerance mechanism contributing to yield.

Genetic Mapping Identifies Consistent Quantitative Trait Loci for Yield Traits of Rice under Greenhouse Drought Conditions

“…Phenotyping of 190 F 2:3 progeny lines and the parents for their drought response was done inside the Louisiana State University Agricultural Center's greenhouse at Gourrier Ln, Baton Rouge, LA during spring 2015 and fall 2017 as previously described [25,28]. Briefly, two sets of six plants per line including parents were grown in 2.8 L plastic pots with bottom holes under normal irrigation.…”

“…Following drought, irrigation was resumed until grain maturity. The experiment was conducted in a complete randomized block design, with three replications in ceramic trays (blocks), as described earlier [25]. Data were recorded on both control and recovered plants for yield traits such as the number of panicles per plant, the number of grains per panicle, and grain yield (g) per plant.…”

“…Phenotypic data were analyzed using the basic R v3.4.1 package and SAS 9.3 [29] as described earlier [25,30]. Normality of the data was determined by the Shapiro-Wilk test and Pearson's test was conducted to estimate the correlations among the yield traits [30].…”

“…Markers used for genotyping consisted of 134 SSRs [31], four Indel markers [32], and six genic SSRs [25] that were polymorphic between Cocodrie and N22. In addition, eight polymorphic SNPs were used to narrow down the gaps in the QTL regions in chromosome 1, 8, and 11.…”

“…Considering the narrow genetic base and drought sensitivity of the U.S. rice germplasm [24], introgression of drought-tolerant genes from drought-tolerant germplasm have been initiated into the background of rice varieties adapted to the southern U.S. [5,25]. Previously, we reported six QTLs (three on chromosome 1 and one each on chromosome 5, 8, and 9) contributing to grain yield under controlled greenhouse conditions, where the favorable alleles for four QTLs were contributed by the drought-tolerant donor variety Vandana [25]. Here, we report on the identification of genetic determinants for grain yield traits under greenhouse drought conditions in the same U.S. genetic background Cocodrie but with a different drought-resistant donor, Nagina 22.…”