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Fulltext Pyramiding of drought yield QTLs into a high quality Malaysian rice cultivar MRQ74 improves yield under reproductive stage drought

Shamsudin NAA, Swamy BPM, Ratnam W, Sta Cruz MT, Sandhu N, Raman AK, et al.

Rice (N Y), 2016 Dec;9(1):21.
PMID: 27164982 DOI: 10.1186/s12284-016-0093-6

BACKGROUND: With the objective of improving the grain yield (GY) of the Malaysian high quality rice cultivar MRQ74 under reproductive stage drought stress (RS), three drought yield QTLs, viz. qDTY 2.2, qDTY 3.1 , and qDTY 12.1 were pyramided by marker assisted breeding (MAB). Foreground selection using QTL specific markers, recombinant selection using flanking markers, and background selections were performed in every generation. BC1F3 derived pyramided lines (PLs) with different combinations of qDTY 2.2, qDTY 3.1 , and qDTY 12.1 were evaluated under both RS and non-stress (NS) during the dry season (DS) of 2013 and 2014 at IRRI.
RESULTS: The GY reductions in RS trials compared to NS trials ranged from 79 to 99 %. Plant height (PH) was reduced and days to flowering (DTF) was delayed under RS. Eleven BC1F5 MRQ74 PLs with yield advantages of 1009 to 3473 kg ha(-1) under RS and with yields equivalent to MRQ74 under NS trials were identified as promising drought tolerance PLs. Five best PLs, IR 98010-126-708-1-4, IR 98010-126-708-1-3, IR 98010-126-708-1-5, IR 99616-44-94-1-1, and IR 99616-44-94-1-2 with a yield advantage of more than 1000 kg ha(-1) under RS and with yield potential equivalent to that of MRQ74 under NS were selected. The effect of three drought grain yield QTLs under RS in MRQ74 was validated. Under NS, PLs with two qDTY combinations (qDTY 2.2 + qDTY 12.1 ) performed better than PLs with other qDTY combinations, indicating the presence of a positive interaction between qDTY 2.2 and qDTY 12.1 in the MRQ74 background.
CONCLUSION: Drought tolerant MRQ74 PLs with a yield advantage of more than 1000 kg ha(-1) under RS were developed. Differential yield advantages of different combinations of the qDTYs indicate a differential synergistic relationship among qDTYs.
Fulltext Association Mapping of Yield and Yield-related Traits Under Reproductive Stage Drought Stress in Rice (Oryza sativa L.)

Swamy BPM, Shamsudin NAA, Rahman SNA, Mauleon R, Ratnam W, Sta Cruz MT, et al.

Rice (N Y), 2017 Dec;10(1):21.
PMID: 28523639 DOI: 10.1186/s12284-017-0161-6

BACKGROUND: The identification and introgression of major-effect QTLs for grain yield under drought are some of the best and well-proven approaches for improving the drought tolerance of rice varieties. In the present study, we characterized Malaysian rice germplasm for yield and yield-related traits and identified significant trait marker associations by structured association mapping.
RESULTS: The drought screening was successful in screening germplasm with a yield reduction of up to 60% and heritability for grain yield under drought was up to 78%. There was a wider phenotypic and molecular diversity within the panel, indicating the suitability of the population for quantitative trait loci (QTL) mapping. Structure analyses clearly grouped the accessions into three subgroups with admixtures. Linkage disequilibrium (LD) analysis revealed that LD decreased with an increase in distance between marker pairs and the LD decay varied from 5-20 cM. The Mixed Linear model-based structured association mapping identified 80 marker trait associations (MTA) for grain yield (GY), plant height (PH) and days to flowering (DTF). Seven MTA were identified for GY under drought stress, four of these MTA were consistently identified in at least two of the three analyses. Most of these MTA identified were on chromosomes 2, 5, 10, 11 and 12, and their phenotypic variance (PV) varied from 5% to 19%. The in silico analysis of drought QTL regions revealed the association of several drought-responsive genes conferring drought tolerance. The major-effect QTLs are useful in marker-assisted QTL pyramiding to improve drought tolerance.
CONCLUSION: The results have clearly shown that structured association mapping is one of the feasible options to identify major-effect QTLs for drought tolerance-related traits in rice.
Elevated CO2 Priming as a Sustainable Approach to Increasing Rice Tiller Number and Yield Potential

Sloan JM, Mujab AAM, Mashitah J, Zulkarami B, Wilson MJ, Toh LS, et al.

Rice (N Y), 2023 Mar 22;16(1):16.
PMID: 36947269 DOI: 10.1186/s12284-023-00629-0

Tillering and yield are linked in rice, with significant efforts being invested to understand the genetic basis of this phenomenon. However, in addition to genetic factors, tillering is also influenced by the environment. Exploiting experiments in which seedlings were first grown in elevated CO2 (eCO2) before transfer and further growth under ambient CO2 (aCO2) levels, we found that even moderate exposure times to eCO2 were sufficient to induce tillering in seedlings, which was maintained in plants grown to maturity plants in controlled environment chambers. We then explored whether brief exposure to eCO2 (eCO2 priming) could be implemented to regulate tiller number and yield in the field. We designed a cost-effective growth system, using yeast to increase the CO2 level for the first 24 days of growth, and grew these seedlings to maturity in semi-field conditions in Malaysia. The increased growth caused by eCO2 priming translated into larger mature plants with increased tillering, panicle number, and improved grain filling and 1000 grain weight. In order to make the process more appealing to conventional rice farmers, we then developed a system in which fungal mycelium was used to generate the eCO2 via respiration of sugars derived by growing the fungus on lignocellulosic waste. Not only does this provide a sustainable source of CO2, it also has the added financial benefit to farmers of generating economically valuable oyster mushrooms as an end-product of mycelium growth. Our experiments show that the system is capable of generating sufficient CO2 to induce increased tillering in rice seedlings, leading eventually to 18% more tillers and panicles in mature paddy-grown crop. We discuss the potential of eCO2 priming as a rapidly implementable, broadly applicable and sustainable system to increase tillering, and thus yield potential in rice.
Fulltext Marker-assisted selection strategy to pyramid two or more QTLs for quantitative trait-grain yield under drought

Kumar A, Sandhu N, Dixit S, Yadav S, Swamy BPM, Shamsudin NAA

Rice (N Y), 2018 May 29;11(1):35.
PMID: 29845495 DOI: 10.1186/s12284-018-0227-0

BACKGROUND: Marker-assisted breeding will move forward from introgressing single/multiple genes governing a single trait to multiple genes governing multiple traits to combat emerging biotic and abiotic stresses related to climate change and to enhance rice productivity. MAS will need to address concerns about the population size needed to introgress together more than two genes/QTLs. In the present study, grain yield and genotypic data from different generations (F3 to F8) for five marker-assisted breeding programs were analyzed to understand the effectiveness of synergistic effect of phenotyping and genotyping in early generations on selection of better progenies.
RESULTS: Based on class analysis of the QTL combinations, the identified superior QTL classes in F3/BC1F3/BC2F3 generations with positive QTL x QTL and QTL x background interactions that were captured through phenotyping maintained its superiority in yield under non-stress (NS) and reproductive-stage drought stress (RS) across advanced generations in all five studies. The marker-assisted selection breeding strategy combining both genotyping and phenotyping in early generation significantly reduced the number of genotypes to be carried forward. The strategy presented in this study providing genotyping and phenotyping cost savings of 25-68% compared with the traditional marker-assisted selection approach. The QTL classes, Sub1 + qDTY 1.1 + qDTY 2.1 + qDTY 3.1 and Sub1 + qDTY 2.1 + qDTY 3.1 in Swarna-Sub1, Sub1 + qDTY 1.1 + qDTY 1.2 , Sub1 + qDTY 1.1 + qDTY 2.2 and Sub1 + qDTY 2.2 + qDTY 12.1 in IR64-Sub1, qDTY 2.2 + qDTY 4.1 in Samba Mahsuri, Sub1 + qDTY 3.1 + qDTY 6.1 + qDTY 6.2 and Sub1 + qDTY 6.1 + qDTY 6.2 in TDK1-Sub1 and qDTY 12.1 + qDTY 3.1 and qDTY 2.2 + qDTY 3.1 in MR219 had shown better and consistent performance under NS and RS across generations over other QTL classes.
CONCLUSION: "Deployment of this procedure will save time and resources and will allow breeders to focus and advance only germplasm with high probability of improved performance. The identification of superior QTL classes and capture of positive QTL x QTL and QTL x background interactions in early generation and their consistent performance in subsequent generations across five backgrounds supports the efficacy of a combined MAS breeding strategy".
Fulltext Photoprotection as a Trait for Rice Yield Improvement: Status and Prospects

Murchie EH, Ali A, Herman T

Rice (N Y), 2015 Dec;8(1):31.
PMID: 26424004 DOI: 10.1186/s12284-015-0065-2

Solar radiation is essential for photosynthesis and global crop productivity but it is also variable in space and time, frequently being limiting or in excess of plant requirements depending on season, environment and microclimate. Photoprotective mechanisms at the chloroplast level help to avoid oxidative stress and photoinhibition, which is a light-induced reduction in photosynthetic quantum efficiency often caused by damage to photosystem II. There is convincing evidence that photoinhibition has a large impact on biomass production in crops and this may be especially high in rice, which is typically exposed to high tropical light levels. Thus far there has been little attention to photoinhibition as a target for improvement of crop yield. However, we now have sufficient evidence to examine avenues for alleviation of this particular stress and the physiological and genetic basis for improvement in rice and other crops. Here we examine this evidence and identify new areas for attention. In particular we discuss how photoprotective mechanisms must be optimised at both the molecular and the canopy level in order to coordinate with efficient photosynthetic regulation and realise an increased biomass and yield in rice.