scholarly journals Genotyping-by-sequencing based QTL mapping for rice grain yield under reproductive stage drought stress tolerance

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Shailesh Yadav ◽  
Nitika Sandhu ◽  
Vikas Kumar Singh ◽  
Margaret Catolos ◽  
Arvind Kumar
Keyword(s):  
Drought Stress ◽  
Grain Yield ◽  
Genotyping By Sequencing ◽  
High Density ◽  
Reproductive Stage ◽  
Linkage Drag ◽  
Rice Grain ◽  
Early Maturity ◽  
Consistent Effect ◽  
Mapping Populations

Abstract QTLs for rice grain yield under reproductive stage drought stress (qDTY) identified earlier with low density markers have shown linkage drag and need to be fine mapped before their utilization in breeding programs. In this study, genotyping-by-sequencing (GBS) based high-density linkage map of rice was developed using two BC1F3 mapping populations namely Swarna*2/Dular (3929 SNPs covering 1454.68 cM) and IR11N121*2/Aus196 (1191 SNPs covering 1399.68 cM) with average marker density of 0.37 cM to 1.18 cM respectively. In total, six qDTY QTLs including three consistent effect QTLs were identified in Swarna*2/Dular while eight qDTY QTLs including two consistent effect QTLs were identified in IR11N121*2/Aus 196 mapping population. Comparative analysis revealed four stable and novel QTLs (qDTY2.4, qDTY3.3, qDTY6.3, and qDTY11.2) which explained 8.62 to 14.92% PVE. However, one of the identified stable grain yield QTL qDTY1.1 in both the populations was located nearly at the same physical position of an earlier mapped major qDTY QTL. Further, the effect of the identified qDTY1.1 was validated in a subset of lines derived from five mapping populations confirming robustness of qDTY1.1 across various genetic backgrounds/seasons. The study successfully identified stable grain yield QTLs free from undesirable linkages of tall plant height/early maturity utilizing high density linkage maps.

scholarly journals qDTY1.1, a major QTL for rice grain yield under reproductive-stage drought stress with a consistent effect in multiple elite genetic backgrounds

BMC Genetics ◽  
2011 ◽  
Vol 12 (1) ◽  
pp. 89 ◽  
Author(s):  
Prashant Vikram ◽  
BP Swamy ◽  
Shalabh Dixit ◽  
Helal Ahmed ◽  
Ma Teresa Sta Cruz ◽  
...  
Keyword(s):  
Drought Stress ◽  
Grain Yield ◽  
Reproductive Stage ◽  
Rice Grain ◽  
Consistent Effect ◽  
Major Qtl

Grain yield QTLs with consistent-effect under reproductive-stage drought stress in rice

2014 ◽  
Vol 161 ◽  
pp. 46-54 ◽  
Author(s):  
Alvin D. Palanog ◽  
B.P. Mallikarjuna Swamy ◽  
Noraziyah Abd Aziz Shamsudin ◽  
Shalabh Dixit ◽  
Jose E. Hernandez ◽  
...  
Keyword(s):  
Drought Stress ◽  
Grain Yield ◽  
Reproductive Stage ◽  
Consistent Effect

Respon Morfologis dan Ekspresi Gen Aquaporin pada Padi IR 64 yang Mengalami Cekaman Kekeringan pada Fase Reproduktif (Morphological Responses and Aquaporin Gene Expression in Rice IR64 under Drought Stress at the Reproductive Stage)

2018 ◽  
Vol 7 (2) ◽  
Author(s):  
Made Pharmawati ◽  
Ni Nyoman Wirasiti ◽  
Luh Putu Wrasiati
Keyword(s):  
Gene Expression ◽  
Drought Stress ◽  
Real Time ◽  
Real Time Pcr ◽  
Control Plant ◽  
Reproductive Stage ◽  
Limiting Factors ◽  
Rice Grain ◽  
Aquaporin Gene ◽  
Peg Treatment

Abstrak Cekaman kekeringan merupakan faktor pembatas penting bagi pertumbuhan dan produktivitas tanaman termasuk padi.      Penelitian ini bertujuan menganalisis respon padi IR64 terhadap cekaman kekeringan dengan pemberian polietilen glikol (PEG) pada fase reproduktif.  Penelitian juga bertujuan menganalisis ekspresi gen aquaporin akibat cekaman kekeringan.  Bibit padi ditanam dalam pot dan perlakuan PEG dengan konsentrasi 108g/L (-0.25MPa) dan 178g/L (-0.52 MPa) diberikan saat munculnya panikula. Perlakuan diberikan selama 2 minggu, kemudian tanaman disiram kembali.  Ekspresi gen diamati pada akhir perlakuan dengan semi kuantitatif real time PCR.  Ekstraksi RNA menggunakan RNeasy plant mini kit, sedangkan sintesis cDNA menggunakan Transcriptor First Strand cDNA Kit.  Hasil penelitian menunjukkan bahwa jumlah malai dan berat total malai berkurang akibat cekaman kekeringan.  Persentase gabah kosong mencapai 84,6% pada perlakuan PEG-0,52 MPa, sedangkan pada perlakuan PEG -0,25 MPa persentase gabah kosong sebesar 67,8%.  Pada kontrol persentase gabah kosong adalah 10,3%.  Ekspresi gen OsPIP2;7 sedikit menurun pada perlakuan PEG -0,52 MPa.Kata kunci: ekspresi gen, IR64, kekeringan, padi, PEG  Abstract Drought stress is one of the limiting factors of plant growth and productivity including rice.  The aim of this study was to analyze responses of IR64 rice to polyethylene glycol (PEG)-induced-drought stress at the reproductive stage.  This study also aimed to analyze the expression of aquaporin under drought stress.  Rice seedlings were grown in pot system and PEG treatment at concentration of -0.25MPa (108g/L) and -0.52 MPa (178g/L) were given when the panicles arose.  Treatments were conducted for 2 weeks, after that the plants were rewatered.  Gene expression was evaluated at the end of PEG treatment using semi quantitative real time PCR. RNA was extracted using RNeasy plant mini kit, while cDNA synthesis was done using Transcriptor First Strand cDNA Kit.  The results showed that the number and weight of rice ear were less in plant treated with PEG than in control.  The percentage of empty rice grain reached 84.6% at PEG -0.52 MPa, while at PEG -0.25 MPa the percentage of empty grain was 67.8%.  In control plant, the percentage of empty grain was 10.3%.  Drought stress did not alter the expression of OsPIP2;7.  Keywords: drought, gene expression, IR64, PEG, rice

Genetic Dissection of Epistatic Interactions Contributing Grain Yield Variability in Rice under Drought

2021 ◽  
Vol 22 ◽  
Author(s):  
Ratna Rani Majumder ◽  
Nitika Sandhu ◽  
Shailesh Yadav ◽  
Margaret Catolos ◽  
Ma. Teresa Sta. Cruz ◽  
...  
Keyword(s):  
Drought Stress ◽  
Grain Yield ◽  
Genetic Background ◽  
Reproductive Stage ◽  
Yield Variability ◽  
Marker Interval ◽  
Negative Interaction ◽  
Epistatic Interactions ◽  
Lattice Design ◽  
Drought Tolerant

Aims: The aim of the present study was to evaluate the performance of ‘high’-‘low’ yielding pyramided lines (PLs) with the same combinations of qDTYs in Samba Mahsuri, MR219 and IR64-Sub1 genetic backgrounds and understand the genetic interactions of QTL and with genetic background affecting grain yield. Background: Epistasis 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). Objectives: The 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 ii) to understand the effect of epistatic interactions of qDTYs and with genetic background on GY under the differential level of stress iii) to identify the promising drought-tolerant lines with high yield under drought and higher background recovery in different genetic backgrounds. Results: Several 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 in 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. Conclusion: High 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. Methods: The experiments were conducted in 2015DS (dry season), 2015WS (wet season) and 2017 DS at IRRI, Los Baños, Philippines, in a transplanted lowland ecosystem under lowland severe stress (LSS), moderate lowland stress (LMS) and lowland non-stress (LNS). The experiments were laid out in alpha lattice design with two replications.

scholarly journals Genetic Dissection of Grain Yield Component Traits Under High Nighttime Temperature Stress in a Rice Diversity Panel

2021 ◽  
Vol 12 ◽  
Author(s):  
Anuj Kumar ◽  
Chirag Gupta ◽  
Julie Thomas ◽  
Andy Pereira
Keyword(s):  
Heat Stress ◽  
Grain Yield ◽  
Candidate Genes ◽  
Significant Snps ◽  
The United States ◽  
Yield Component ◽  
Reproductive Stage ◽  
Venn Diagram ◽  
Rice Grain ◽  
Diversity Panel

To dissect the genetic complexity of rice grain yield (GY) and quality in response to heat stress at the reproductive stage, a diverse panel of 190 rice accessions in the United States Department of Agriculture (USDA) rice mini-core collection (URMC) diversity panel were treated with high nighttime temperature (HNT) stress at the reproductive stage of panicle initiation. The quantifiable yield component response traits were then measured. The traits, panicle length (PL), and number of spikelets per panicle (NSP) were evaluated in subsets of the panel comprising the rice subspecies Oryza sativa ssp. Indica and ssp. Japonica. Under HNT stress, the Japonica ssp. exhibited lower reductions in PL and NSP and a higher level of genetic variation compared with the other subpopulations. Whole genome sequencing identified 6.5 million single nucleotide polymorphisms (SNPs) that were used for the genome-wide association studies (GWASs) of the PL and NSP traits. The GWAS analysis in the Combined, Indica, and Japonica populations under HNT stress identified 83, 60, and 803 highly significant SNPs associated with PL, compared to the 30, 30, and 11 highly significant SNPs associated with NSP. Among these trait-associated SNPs, 140 were coincident with genomic regions previously reported for major GY component quantitative trait loci (QTLs) under heat stress. Using extents of linkage disequilibrium in the rice populations, Venn diagram analysis showed that the highest number of putative candidate genes were identified in the Japonica population, with 20 putative candidate genes being common in the Combined, Indica and Japonica populations. Network analysis of the genes linked to significant SNPs associated with PL and NSP identified modules that were involved in primary and secondary metabolisms. The findings in this study could be useful to understand the pathways/mechanisms involved in rice GY and its components under HNT stress for the acceleration of rice-breeding programs and further functional analysis by molecular geneticists.

Sensitivities of rice grain yield and other panicle characters to late-stage drought stress revealed by phenotypic correlation and QTL analysis

2009 ◽  
Vol 25 (4) ◽  
pp. 603-613 ◽  
Author(s):  
Guolan Liu ◽  
Hanwei Mei ◽  
Hongyan Liu ◽  
Xinqiao Yu ◽  
Guihua Zou ◽  
...  
Keyword(s):  
Drought Stress ◽  
Grain Yield ◽  
Qtl Analysis ◽  
Late Stage ◽  
Phenotypic Correlation ◽  
Rice Grain

scholarly journals Drought stress during the reproductive stage of two soybean lines

2020 ◽  
Vol 55 ◽  
Author(s):  
Vanessa do Rosário Rosa ◽  
Adinan Alves da Silva ◽  
Danielle Santos Brito ◽  
José Domingos Pereira Júnior ◽  
Cíntia Oliveira Silva ◽  
...  
Keyword(s):  
Drought Stress ◽  
Grain Yield ◽  
Photosynthetic Apparatus ◽  
Field Capacity ◽  
Development Stage ◽  
Reproductive Stage ◽  
Chloroplast Pigments ◽  
Severe Water Deficit ◽  
Effects Of Drought ◽  
Water Limitations

Abstract: The objective of this work was to evaluate the effects of drought stress in the reproductive stage (R3) on the physiological parameters and grain yield of two soybean (Glycine max) lines. The Vx-08-10819 and Vx-08-11614 soybean lines were grown in a greenhouse, where they were irrigated until they reached the R3 development stage. During three days, the weight of the pots was monitored daily in order to maintain 100, 60, and 40% field capacity (control and moderate and severe stress, respectively). The parameters gas exchange and chlorophyll a fluorescence, as well as chloroplast pigments, osmoregulatory solutes and antioxidant enzymes, were determined. After stress, the plants were rehydrated until the end of the reproductive stage (R8), to evaluate grain yield. Vx-08-10819 showed traits that contributed to drought tolerance, such as better water-use efficiency, modulation of leaf area, and enzymatic activity, as well as a more efficient photosynthetic apparatus and a lower lipid peroxidation rate than Vx-08-11614. In addition, Vx-08-10819 maintained its productivity even after the severe water deficit. By contrast, water limitations affected negatively the productivity of Vx-08-11614. The Vx-08-10819 soybean line can efficiently withstand drought periods during the reproductive stage, without any interferences on final grain yield.

A Large-Effect QTL for Grain Yield under Reproductive-Stage Drought Stress in Upland Rice

Crop Science ◽  
2007 ◽  
Vol 47 (2) ◽  
pp. 507-516 ◽  
Author(s):  
Jérôme Bernier ◽  
Arvind Kumar ◽  
Venuprasad Ramaiah ◽  
Dean Spaner ◽  
Gary Atlin
Keyword(s):  
Drought Stress ◽  
Grain Yield ◽  
Upland Rice ◽  
Reproductive Stage

scholarly journals Response of phytohormone homeostasis to heat stress and the roles of phytohormones in rice grain yield: a review

2019 ◽  
Author(s):  
Chao Wu ◽  
She Tang ◽  
Ganghua Li ◽  
Shaohua Wang ◽  
Shah Fahad ◽  
...  
Keyword(s):  
Heat Stress ◽  
Grain Yield ◽  
Grain Filling ◽  
Reproductive Organs ◽  
Reproductive Stage ◽  
Grain Weight ◽  
Rice Grain ◽  
Vascular Bundles ◽  
Rice Varieties ◽  
Heat Effects

Rice is highly susceptible to heat stress at the reproductive stage. In this review, we first summarize recent progress in heat effects on rice grain yield during different reproductive stages. Different responses of yield traits of rice to heat stress during different reproductive stages are identified. The number of spikelets per panicle is reduced by heat stress during the early reproductive stage but is not affected by heat stress during the mid-late reproductive stage. Spikelet sterility induced by heat stress can be attributed primarily to physiological abnormalities in the reproductive organs during flowering but attributed to structural and morphological abnormalities in reproductive organs during panicle initiation. The lower grain weight caused by heat stress during the early reproductive stage was due to a reduction in non-structural carbohydrates, undeveloped vascular bundles, and a reduction in grain length and width, while a shortened grain filling duration, reduced grain filling rate, and decreased grain width affect grain weight when heat stress occurs during grain filling. Phytohormones play vital roles in regulating plant adaptations against heat stress. We discuss the processes involving phytohormone homeostasis (biosynthesis, catabolism, deactivation, and transport) in response to heat stress. It is currently thought that biosynthesis and transport may be the key processes that determine phytohormone levels and final grain yield in rice under heat stress conditions. Finally, we prospect that screening and breeding rice varieties with comprehensive tolerance to heat stress throughout the entire reproductive phase could be feasible to cope with unpredictable heat events in the future. Studies in phytohormone homeostatic response are needed to further reveal the key processes that determine phytohormone levels under heat condition.

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