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ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Publications at this Location » Publication #328264

Title: Genetic and environmental effects in the TeQing-into-Lemont (TIL) population under flooded and alternating wet-dry conditions

item Edwards, Jeremy
item Teaster, Neal
item Scheffler, Brian
item McClung, Anna

Submitted to: Rice Technical Working Group Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 12/22/2015
Publication Date: 7/2/2017
Citation: Edwards, J., Teaster, N.D., Scheffler, B.E., McClung, A.M. 2017. Genetic and environmental effects in the TeQing-into-Lemont (TIL) population under flooded and alternating wet-dry conditions. Proc. 36th Rice Technical Working Group Meeting, Galveston, TX, p. 69-70. March 1-4, 2016. CDROM.

Interpretive Summary:

Technical Abstract: Over the last decade there has been growing concern regarding sustainability of US rice production due to multi-year droughts and depletion of ground water resources. There is a need for research to develop rice varieties that are optimized for production using less irrigation water. One rice production system that has been found to use less irrigation water is intermittent flooding, also known as alternate wetting-drying (AWD). Although adjustments may need to be made regarding weed management, nutrient utilization, and disease control, without season long flooding, AWD is a viable option that is being used in regions of the world where indica germplsm is grown. Currently, there has been limited research in the USA on the role of genetics in controlling yield response under AWD systems. The goal of this study is to use a set of indica into tropical japonica chromosome segment substitution lines (CSSLs) to 1) assess the impact of indica introgressions on yield components when grown under the AWD system, 2) evaluate the genetic by environment (GxE) effects between the two systems, and 3) identify candidate loci/genes that may be useful for maintaining or improving yield under AWD. The rice (Oryza sativa L.) population used in this study consists of 123 CSSLs developed by backcrossing the indica donor parent “TeQing” with the tropical japonica recurrent parent “Lemont.” The study was conducted over two growing seasons in Stuttgart, AR. The two irrigation treatments included the typical season long flood and an AWD system in adjacent fields. Plots were arranged in randomized block design with four replications. Each plot consisted of a single row of ~ 10 plants seeded in hill plots on 30 cm centers. After stand establishment, the AWD field was allowed to dry to approximately 22% before it was reflooded. The flood remained for 3 days then the field was drained and allowed to dry to 22 % soil moisture before repeating the cycle. Two representative plants from each plot were tagged at the early tillering stage and were monitored throughout the season prior to harvest. Phenotypic traits assessed included plant height, days to heading (DTH) , number of tillers, number of panicles, number of mature panicles, main panicle length, number of unfilled (blank) panicles, number of seeds per main panicle, weight of seed on main panicle, weight of 100 seed, total yield per plant, and kernel characteristics. The latter included length, width, and % chalk as determined on brown rice using an image analysis system. Temperature and rainfall were tracked on site by two weather stations. In addition, leaf surface temperature of the parentals was measured using a thermal imager for multiple leaves from each plant taken along the middle portion of the leaf blade whose surfaces faced the camera. The CSSLs were previously genotyped with 178 SSR markers. Many background introgressions were detected by single SSRs, suggesting that higher genotyping coverage could reveal additional background introgressions and better define the size of previously detected introgressions. Thus, for this study, the CSSLs were re-genotyped using genotyping-by-sequencing (GBS) to gain higher marker coverage, DNA was extracted and barcoded GBS libraries were prepared and sequenced on 2 lanes of an Illumina HiSeq2500. The statistical model tested the effects due to genotype, year, replications, and irrigation treatment as well as interactions between genotype by treatment, and genotype by year. For the mapping parents, Teqing and Lemont, the genotype effect was significant for all traits (14/14). The year effect was significant for all traits except kernel length and width (12/14). The irrigation effect was significant for DTH, height, kernel length and width, 100 seed weight, primary panicle seed weight, and total yield. There were significant genotype by irrigation interacti