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Epistatic interactions of major effect drought QTLs with genetic background loci determine grain yield of rice under drought stress.

ABSTRACT: Epistatic interactions of QTLs with the genetic background and QTL-QTL interaction plays an important role in the phenotypic performance of introgression lines developed through genomic-assisted breeding (GAB). In this context, NIL pairs developed with various drought QTL (qDTY) combinations in the genetic background of IR64, TDK1-Sub1 and Savitri backgrounds were utilized to study the interactions. Multi-season phenotyping of NIL pairs harboring similar qDTY combinations provided contrasting performance for grain yield under drought (RS) (classified as high and low yielding NILs) but nearly similar performance under non-stress(NS) conditions. Genome wide genotyping data revealed a total of 16, 5 and 6 digenic interactions were detected under RS conditions in low yielding NILs of IR64, TDK1-Sub1 and Savitri respectively while no significant interaction was found in high yielding NILs under RS and NS conditions in any of the genetic backgrounds used in this study. It is evident from this study that existence of epistatic interactions between QTLs with genetic background, QTL-QTL interaction and interactions among background markers loci itself on different chromosomes influences the expression of a complex trait such as grain yield under drought. The generated information will be useful in all the GAB program of across the crops for precise breeding.

SUBMITTER: Yadav S

PROVIDER: S-EPMC6385343 | biostudies-literature | 2019 Feb

REPOSITORIES: biostudies-literature

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Epistatic interactions of major effect drought QTLs with genetic background loci determine grain yield of rice under drought stress.

Yadav Shailesh S Sandhu Nitika N Majumder Ratna Rani RR Dixit Shalabh S Kumar Santosh S Singh S P SP Mandal N P NP Das S P SP Yadaw Ram Baran RB Singh Vikas Kumar VK Sinha Pallavi P Varshney Rajeev K RK Kumar Arvind A

Scientific reports 20190222 1

Epistatic interactions of QTLs with the genetic background and QTL-QTL interaction plays an important role in the phenotypic performance of introgression lines developed through genomic-assisted breeding (GAB). In this context, NIL pairs developed with various drought QTL (qDTY) combinations in the genetic background of IR64, TDK1-Sub1 and Savitri backgrounds were utilized to study the interactions. Multi-season phenotyping of NIL pairs harboring similar qDTY combinations provided contrasting pe ...[more]

PMID: 30796339

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Project description:AimsThe aim of the present study was to evaluate the performance of 'high'-'low' yielding pyramided lines (PLs), having the same combinations of qDTYs in Samba Mahsuri, MR219 and IR64-Sub1 genetic backgrounds, and to understand the genetic interactions among QTL and/with genetic background affecting grain yield.BackgroundEpistasis regulates the expression of traits governed by several major/minor genes/QTL. Multiple pyramided lines (PLs) with the same grain yield QTL (qDTYs) combinations but possessing grain yield variability under different levels of reproductive stage drought stress were identified in different rice genetic backgrounds at International Rice Research Institute (IRRI).ObjectivesThe objectives of the present study were to evaluate the performance pyramided lines (PLs) with drought QTL in the backgrounds of Samba Mahsuri, MR219 and IR64-Sub1 under reproductive stage drought stress (RS) and NS (non-stress) conditions, to understand the effect of epistatic interactions among qDTYs and with genetic background on GY under the differential level of stress and to identify the promising drought-tolerant lines with high yield under drought and higher background recovery in different genetic backgrounds.MethodsThe experiments were conducted in 2015 DS (dry season), 2015 WS (wet season) and 2017 DS at IRRI, Los Baños, Philippines, in a transplanted lowland ecosystem under lowland severe stress (LSS), lowland moderate stress (LMS) and lowland non-stress (LNS). The experiments were laid out in alpha lattice design with two replications.ResultsSeveral digenic interactions were found in different genetic backgrounds, 13 interactions in Samba Mahsuri, 11 in MR219 and 20 in IR64-Sub1 backgrounds. Among all digenic interactions, one QTL × QTL interaction, 17 QTL × background and 26 background × background interactions resulted in GY reduction in low yielding PLs in different genetic backgrounds under LSS or LMS. Negative interaction of qDTY3.1 , qDTY4.1 and qDTY9.1 with background markers and background × background interactions caused up to 15% GY reduction compared to the high yielding PLs under LMS in the Samba Mahsuri PLs. In MR219 PLs, the negative interaction of qDTY2.2 , qDTY3.2 , qDTY4.1 and qDTY12.1 with the background marker interval RM314-RM539, RM273-RM349 and RM445-RM346, RM473D-RM16, respectively resulted 52% GY reduction compared to the high yielding PLs under LSS. In IR64-Sub1 PLs, qDTY6.1 interacted with background loci at RM16-RM135, RM228-RM333, RM202-RM287 and RM415-RM558A marker interval under LSS and at RM475-RM525 marker interval under LMS, causing GY reduction to 58% compared to the high yielding PLs.ConclusionHigh yielding PLs in Samba Mahsuri (IR 99734:1-33-69-1-22-6), MR219 (IR 99784-156-87-2-4-1) and IR64-Sub1 (IR 102784:2-89-632-2-1-2) backgrounds without any negative interactions were identified. The identified selected promising PLs may be used as potential drought-tolerant donors or may be released as varieties for drought-prone ecosystems in different countries.

Project description:BACKGROUND: Selection for grain yield under drought is an efficient criterion for improving the drought tolerance of rice. Recently, some drought-tolerant rice varieties have been developed using this selection criterion and successfully released for cultivation in drought-prone target environments. The process can be made more efficient and rapid through marker-assisted breeding, a well-known fast-track approach in crop improvement. QTLs have been identified for grain yield under drought with large effects against drought-susceptible varieties. Most of the identified QTLs show large QTL?×?environment or QTL?×?genetic background interactions. The development of mapping populations in the background of popular high-yielding varieties, screening across environments, including the target environments, and the identification of QTLs with a consistent effect across environments can be a suitable alternative marker-assisted breeding strategy. An IR74371-46-1-1?×?Sabitri backcross inbred line population was screened for reproductive-stage drought stress at the International Rice Research Institute, Philippines, and Regional Agricultural Research Station, Nepalgunj, Nepal, in the dry and wet seasons of 2011, respectively. A bulk segregant analysis approach was used to identify markers associated with high grain yield under drought. RESULTS: A QTL, qDTY12.1, significantly associated with grain yield under reproductive-stage drought stress was identified on chromosome 12 with a consistent effect in two environments: IRRI, Philippines, and RARS, Nepalgunj, Nepal. This QTL explained phenotypic variance of 23.8% and contributed an additive effect of 45.3% for grain yield under drought. The positive QTL allele for qDTY12.1 was contributed by tolerant parent IR74371-46-1-1. CONCLUSIONS: In this study, qDTY12.1 showed a consistent effect across environments for high grain yield under lowland reproductive-stage drought stress in the background of popular high-yielding but drought-susceptible recipient variety Sabitri. qDTY12.1 was also reported previously [Crop Sci 47:507-516, 2007] to increase grain yield under upland reproductive-stage drought stress situations. qDTY12.1 is the only QTL reported so far in rice to have shown a large effect against multiple recipient genetic backgrounds as well as under highly diverse upland and lowland rice ecosystems. qDTY12.1 can be successfully introgressed to improve grain yield under drought of popular high-yielding but drought-susceptible lowland as well as upland adapted varieties following marker-assisted breeding.

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Epistatic interactions of major effect drought QTLs with genetic background loci determine grain yield of rice under drought stress.

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Epistatic interactions of major effect drought QTLs with genetic background loci determine grain yield of rice under drought stress.

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