scholarly journals Identification of novel QTLs for grain fertility and associated traits to decipher poor grain filling of basal spikelets in dense panicle rice

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sudhanshu Sekhar ◽  
Jitendra Kumar ◽  
Soumya Mohanty ◽  
Niharika Mohanty ◽  
Rudraksh Shovan Panda ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Ethylene Production ◽  
Recombinant Inbred Lines ◽  
Grain Filling ◽  
Spikelet Fertility ◽  
Rice Cultivars ◽  
Spikelet Number ◽  
Spikelet Sterility ◽  
Ubiquitin Protein Ligase ◽  
Comparative Expression Analysis

AbstractHigh grain number is positively correlated with grain yield in rice, but it is compromised because of poor filling of basal spikelets in dense panicle bearing numerous spikelets. The phenomenon that turns the basal spikelets of compact panicle sterile in rice is largely unknown. In order to understand the factor(s) that possibly determines such spikelet sterility in compact panicle cultivars, QTLs and candidate genes were identified for spikelet fertility and associated traits like panicle compactness, and ethylene production that significantly influences the grain filling using recombinant inbred lines developed from a cross between indica rice cultivars, PDK Shriram (compact, high spikelet number) and Heera (lax, low spikelet number). Novel QTLs, qSFP1.1, qSFP3.1, and qSFP6.1 for spikelet fertility percentage; qIGS3.2 and qIGS4.1 for panicle compactness; and qETH1.2, qETH3.1, and qETH4.1 for ethylene production were consistently identified in both kharif seasons of 2017 and 2018. The comparative expression analysis of candidate genes like ERF3, AP2-like ethylene-responsive transcription factor, EREBP, GBSS1, E3 ubiquitin-protein ligase GW2, and LRR receptor-like serine/threonine-protein kinase ERL1 associated with identified QTLs revealed their role in poor grain filling of basal spikelets in a dense panicle. These candidate genes thus could be important for improving grain filling in compact-panicle rice cultivars through biotechnological interventions.

Identification of Novel QTLs for Spikelet Fertility, Panicle Compactness and Phytohormone Ethylene to Decipher Poor Grain Filling of Basal Spikelets in Dense Panicle Rice

2021 ◽  
Author(s):  
Sudhanshu Sekhar ◽  
Jitendra Kumar ◽  
Soumya Mohanty ◽  
Niharika Mohanty ◽  
Rudraksh Shovan Panda ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Ethylene Production ◽  
Recombinant Inbred Lines ◽  
Grain Filling ◽  
Spikelet Fertility ◽  
Rice Cultivars ◽  
Spikelet Number ◽  
Spikelet Sterility ◽  
Ubiquitin Protein Ligase ◽  
Comparative Expression Analysis

Abstract High grain number is positively correlated with grain yield in rice, but it is compromised because of poor filling of basal spikelets in dense panicle bearing numerous spikelets. The phenomenon that turns the basal spikelets of compact panicle sterile in rice is largely unknown. In order to understand the factor(s) that possibly determines such spikelet sterility in compact panicle cultivars, QTLs and candidate genes were identified for spikelet fertility percentage, panicle compactness and ethylene production that significantly influence the grain filling using recombinant inbred lines developed from a cross between indica rice cultivars, PDK Shriram (compact, high spikelet number) and Heera (lax, low spikelet number). Novel QTLs, qSFP1.1, qSFP3.1 and qSFP6.1 for spikelet fertility percentage; qIGS3.2 and qIGS4.1 for panicle compactness; and qETH1.2, qETH3.1 and qETH4.1 for ethylene production were consistently identified in both kharif seasons of 2017 and 2018. The comparative expression analysis of candidate genes like ERF3, AP2-like ethylene-responsive transcription factor, EREBP, GBSS1, E3 ubiquitin-protein ligase GW2, and LRR receptor-like serine/threonine-protein kinase ERL1 associated with identified QTLs revealed their role in poor grain filling of basal spikelets in dense panicle. These candidate genes thus could be important for improving grain filling in compact-panicle rice cultivars through biotechnological interventions.

scholarly journals Introgression of Sub1 (SUB1) QTL in mega rice cultivars increases ethylene production to the detriment of grain- filling under stagnant flooding

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Sandhya Rani Kuanar ◽  
Kutubuddin Ali Molla ◽  
Krishnendu Chattopadhyay ◽  
Ramani Kumar Sarkar ◽  
Pravat Kumar Mohapatra
Keyword(s):  
Grain Yield ◽  
Ethylene Production ◽  
Stem Elongation ◽  
Starch Synthesis ◽  
Acc Oxidase ◽  
Acc Synthase ◽  
Grain Filling ◽  
Soluble Carbohydrates ◽  
Rice Cultivars ◽  
Oxidase Enzyme

AbstractIn the recent time, Submergence1 (Sub1)QTL, responsible for imparting tolerance to flash flooding, has been introduced in many rice cultivars, but resilience of the QTL to stagnant flooding (SF) is not known. The response of Sub1-introgression has been tested on physiology, molecular biology and yield of two popular rice cultivars (Swarna and Savitri) by comparison of the parental and Sub1-introgression lines (SwarnaSub1 and SavitriSub1) under SF. Compared to control condition SF reduced grain yield and tiller number and increased plant height and Sub1- introgression mostly matched these effects. SF increased ethylene production by over-expression of ACC-synthase and ACC-oxidase enzyme genes of panicle before anthesis in the parental lines. Expression of the genes changed with Sub1-introgression, where some enzyme isoform genes over-expressed after anthesis under SF. Activities of endosperm starch synthesizing enzymes SUS and AGPase declined concomitantly with rise ethylene production in the Sub1-introgressed lines resulting in low starch synthesis and accumulation of soluble carbohydrates in the developing spikelets. In conclusion, Sub1-introgression into the cultivars increased susceptibility to SF. Subjected to SF, the QTL promoted genesis of ethylene in the panicle at anthesis to the detriment of grain yield, while compromising with morphological features like tiller production and stem elongation.

scholarly journals Screening and identification of genes affecting grain quality and spikelet fertility during high-temperature treatment in grain filling stage of rice

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Jae-Ryoung Park ◽  
Eun-Gyeong Kim ◽  
Yoon-Hee Jang ◽  
Kyung-Min Kim
Keyword(s):  
High Temperature ◽  
Candidate Genes ◽  
High Temperatures ◽  
Grain Quality ◽  
Grain Filling ◽  
Temperature Treatment ◽  
Spikelet Fertility ◽  
High Temperature Treatment ◽  
Rice Varieties ◽  
Grain Filling Stage

Abstract Background Recent temperature increases due to rapid climate change have negatively affected rice yield and grain quality. Particularly, high temperatures during right after the flowering stage reduce spikelet fertility, while interfering with sugar energy transport, and cause severe damage to grain quality by forming chalkiness grains. The effect of high-temperature on spikelet fertility and grain quality during grain filling stage was evaluated using a double haploid line derived from another culture of F1 by crossing Cheongcheong and Nagdong cultivars. Quantitative trait locus (QTL) mapping identifies candidate genes significantly associated with spikelet fertility and grain quality at high temperatures. Results Our analysis screened OsSFq3 that contributes to spikelet fertility and grain quality at high-temperature. OsSFq3 was fine-mapped in the region RM15749-RM15689 on chromosome 3, wherein four candidate genes related to the synthesis and decomposition of amylose, a starch component, were predicted. Four major candidate genes, including OsSFq3, and 10 different genes involved in the synthesis and decomposition of amylose and amylopectin, which are starch constituents, together with relative expression levels were analyzed. OsSFq3 was highly expressed during the initial stage of high-temperature treatment. It exhibited high homology with FLOURY ENDOSPERM 6 in Gramineae plants and is therefore expected to function similarly. Conclusion The QTL, major candidate genes, and OsSFq3 identified herein could be effectively used in breeding rice varieties to improve grain quality, while tolerating high temperatures, to cope with climate changes. Furthermore, linked markers can aid in marker-assisted selection of high-quality and -yield rice varieties tolerant to high temperatures.

Corrigendum to: Controlling the trade-off between spikelet number and grain filling: the hierarchy of starch synthesis in spikelets of rice panicle in relation to hormone dynamics

2019 ◽  
Vol 46 (6) ◽  
pp. 595 ◽  
Author(s):  
Rashmi Panigrahi ◽  
Ekamber Kariali ◽  
Binay Bhusan Panda ◽  
Tanguy Lafarge ◽  
Pravat Kumar Mohapatra
Keyword(s):  
Ethylene Production ◽  
Starch Synthesis ◽  
Grain Filling ◽  
Starch Biosynthesis ◽  
Yield Potential ◽  
Human Consumption ◽  
Spikelet Number ◽  
Trade Off ◽  
Inferior Spikelets ◽  
Endosperm Starch

The advent of dwarf statured rice varieties enabled a major breakthrough in yield and production, but raising the ceiling of genetically determined yield potential even further has been the breeding priority. Grain filling is asynchronous in the rice panicle; the inferior spikelets particularly on secondary branches of the basal part do not produce grains of a quality suitable for human consumption. Of the various strategies being considered, the control of ethylene production at anthesis has been a valuable route to potentially enhance genetic yield level of rice. The physiology underlying spikelet development has revealed spikelet position-specific ethylene levels determine the extent of grain filling, with higher levels resulting in ill-developed spikelet embodying poor endosperm starch content. To break the yield barrier, breeders have increased spikelet number per panicle in new large-panicle rice plants. However, the advantage of panicles with numerous spikelets has not resulted in enhanced yield because of poor filling of inferior spikelets. High spikelet number stimulates ethylene production and downgrading of starch synthesis, suggesting a trade-off between spikelet number and grain filling. High ethylene production in inferior spikelets suppresses expression of genes encoding endosperm starch synthesising enzymes. Hence, ethylene could be a retrograde signal that dictates the transcriptome dynamics for the cross talk between spikelet number and grain filling in the rice panicle, so attenuation of its activity may provide a solution to the problem of poor grain filling in large-panicle rice. This physiological linkage that reduces starch biosynthesis of inferior kernels is not genetically constitutive and amenable for modification through chemical, biotechnological, surgical and allelic manipulations. Studies on plant genotypes with different panicle architecture have opened up possibilities of selectively improving starch biosynthesis of inferior spikelets and thereby increasing grain yield through a physiological route.

Controlling the trade-off between spikelet number and grain filling: the hierarchy of starch synthesis in spikelets of rice panicle in relation to hormone dynamics

2019 ◽  
Vol 46 (6) ◽  
pp. 507 ◽  
Author(s):  
Rashmi Panigrahi ◽  
Ekamber Kariali ◽  
Binay Bhusan Panda ◽  
Tanguy Lafarge ◽  
Pravat Kumar Mohapatra
Keyword(s):  
Ethylene Production ◽  
Starch Synthesis ◽  
Grain Filling ◽  
Starch Biosynthesis ◽  
Yield Potential ◽  
Human Consumption ◽  
Spikelet Number ◽  
Trade Off ◽  
Inferior Spikelets ◽  
Endosperm Starch

The advent of dwarf statured rice varieties enabled a major breakthrough in yield and production, but raising the ceiling of genetically determined yield potential even further has been the breeding priority. Grain filling is asynchronous in the rice panicle; the inferior spikelets particularly on secondary branches of the basal part do not produce grains of a quality suitable for human consumption. Of the various strategies being considered, the control of ethylene production at anthesis has been a valuable route to potentially enhance genetic yield level of rice. The physiology underlying spikelet development has revealed spikelet position-specific ethylene levels determine the extent of grain filling, with higher levels resulting in ill-developed spikelet embodying poor endosperm starch content. To break the yield barrier, breeders have increased spikelet number per panicle in new large-panicle rice plants. However, the advantage of panicles with numerous spikelets has not resulted in enhanced yield because of poor filling of inferior spikelets. High spikelet number stimulates ethylene production and downgrading of starch synthesis, suggesting a trade-off between spikelet number and grain filling. High ethylene production in inferior spikelets suppresses expression of genes encoding endosperm starch synthesising enzymes. Hence, ethylene could be a retrograde signal that dictates the transcriptome dynamics for the cross talk between spikelet number and grain filling in the rice panicle, so attenuation of its activity may provide a solution to the problem of poor grain filling in large-panicle rice. This physiological linkage that reduces starch biosynthesis of inferior kernels is not genetically constitutive and amenable for modification through chemical, biotechnological, surgical and allelic manipulations. Studies on plant genotypes with different panicle architecture have opened up possibilities of selectively improving starch biosynthesis of inferior spikelets and thereby increasing grain yield through a physiological route.

scholarly journals Screening and Identification of Genes Affecting Grain Quality and Spikelet Fertility During High-Temperature Treatment in Grain Filling Stage of Rice

2021 ◽  
Author(s):  
Jae-Ryoung Park ◽  
Eun-Gyeong Kim ◽  
Yoon-Hee Jang ◽  
Kyung-Min Kim
Keyword(s):  
High Temperature ◽  
Candidate Genes ◽  
High Temperatures ◽  
Grain Quality ◽  
Grain Filling ◽  
Temperature Treatment ◽  
Spikelet Fertility ◽  
High Temperature Treatment ◽  
Rice Varieties ◽  
Filling Stage

Abstract Background Recent temperature increases due to rapid climate change have negatively affected rice yield and grain quality. Particularly, high temperatures during rice filling stage from the flowering stage reduce spikelet fertility, while interfering with sugar energy transport, and cause severe damage to grain quality by forming chalkiness grains. The effect of high-temperature on spikelet fertility and grain quality during grain filling stage was evaluated using a double haploid line derived from anther culture of F1 by crossing Cheongcheong and Nagdong cultivars. Quantitative trait locus (QTL) mapping identifies candidate genes significantly associated with spikelet fertility and grain quality at high temperatures. Results Our analysis screened OsSFq3 that contributes to spikelet fertility and grain quality at high-temperature. OsSFq3 was fine-mapped in the region RM15749-RM15689 on chromosome 3, wherein four candidate genes related to the synthesis and decomposition of amylose, a starch component, were predicted. Four major candidate genes, including OsSFq3, and 10 different genes involved in the synthesis and decomposition of amylose and amylopectin, which are starch constituents, together with relative expression levels were analyzed. OsSFq3 was highly expressed during the initial stage of high-temperature treatment. It exhibited high homology with FLOURY ENDOSPERM 6 in Gramineae plants and is therefore expected to function similarly. Conclusion The QTL, major candidate genes, and OsSFq3 identified herein could be effectively used in breeding rice varieties to improve grain quality, while tolerating high temperatures, to cope with climate changes. Furthermore, linked markers can aid in marker-assisted selection of high-quality and -yield rice varieties tolerant to high temperatures.

Compact panicle architecture is detrimental for growth as well as sucrose synthase activity of developing rice kernels

2015 ◽  
Vol 42 (9) ◽  
pp. 875 ◽  
Author(s):  
B. B. Panda ◽  
A. K. Badoghar ◽  
K. Das ◽  
R. Panigrahi ◽  
E. Kariali ◽  
...  
Keyword(s):  
Sucrose Synthase ◽  
Recombinant Inbred Lines ◽  
Grain Filling ◽  
Active Period ◽  
Rt Pcr ◽  
Spikelet Number ◽  
Genetic Expression ◽  
Starch Concentration ◽  
Carbohydrate Concentration ◽  
Quantitative Appraisal

The increase of spikelet number in the panicles of modern super rice has made the architecture compact, as the extra spikelets are accommodated mostly on secondary branches than on primary branches. However, the grain yield did not improve because of poor grain filling, which was more visible in the basal spikelets than apical spikelets. The objective of this study was to examine the effect of the compactness and positional difference of spikelets in the panicle on grain filling by comparing the activity and genetic expression of starch synthesising enzymes in the developing kernels of lax-(Upahar and CR3856–45–11–2-7–2-5 (CR-45)) and compact-(Mahalaxmi and CR3856–29–14–2-1–1-1 (CR-29)) panicle cultivars. Upahar and Mahalaxmi are genetically related, whereas CR-45 and CR-29 are recombinant inbred lines. The grain carbohydrate concentration and activity of sucrose synthase (SUS) enzyme were estimated during the active period of grain filling. Further, expression of isoforms of SUS, ADP glucose pyrophosphorylase (APL and APS for large and small units respectively) and starch synthase (SS and GBSS for soluble and granule bound starch synthases respectively) were also assayed through PCR studies. The genotype approach used revealed grain SUS activity and starch concentration high and sugar concentration low in the lax- compared with compact-panicle cultivars and in the apical spikelets compared with basal ones. The margin of variation between apical and basal spikelets was higher in the compact- than the lax-panicle cultivars. Genetic expression of most of the isoforms of the enzymes was higher in the lax- than the compact-panicle cultivars as seen in RT–PCR studies. A quantitative appraisal of transcript levels of isoforms in the qRT–PCR identified greater expression of SUS3 in the basal spikelets of Upahar than that in Mahalaxmi and in CR-45 over CR-29, most prominently during the active period of grain filling. We conclude that proximal location as well as increased density of spikelets on panicles affected SUS3 expression in the basal spikelets. The metabolic dominance of a spikelet in rice panicle is dependent on the expression of the genes for different isoforms of starch synthesising enzymes, but the expression of SUS3 could be more specific than the others. SUS3 expression is most active during grain filling of the lax-panicle cultivars, but its dominance is reduced significantly in the kernels of the compact-panicle cultivars.

scholarly journals QTL Analysis of Five Morpho-Physiological Traits in Bread Wheat Using Two Mapping Populations Derived from Common Parents

Genes ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 604
Author(s):  
Paolo Vitale ◽  
Fabio Fania ◽  
Salvatore Esposito ◽  
Ivano Pecorella ◽  
Nicola Pecchioni ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Recombinant Inbred Lines ◽  
Snp Array ◽  
Heading Date ◽  
Tiller Number ◽  
Genetic Maps ◽  
Yield Potential ◽  
Adaptation To Climate Change ◽  
Map Resolution ◽  
Mapping Populations

Traits such as plant height (PH), juvenile growth habit (GH), heading date (HD), and tiller number are important for both increasing yield potential and improving crop adaptation to climate change. In the present study, these traits were investigated by using the same bi-parental population at early (F2 and F2-derived F3 families) and late (F6 and F7, recombinant inbred lines, RILs) generations to detect quantitative trait loci (QTLs) and search for candidate genes. A total of 176 and 178 lines were genotyped by the wheat Illumina 25K Infinium SNP array. The two genetic maps spanned 2486.97 cM and 3732.84 cM in length, for the F2 and RILs, respectively. QTLs explaining the highest phenotypic variation were found on chromosomes 2B, 2D, 5A, and 7D for HD and GH, whereas those for PH were found on chromosomes 4B and 4D. Several QTL detected in the early generations (i.e., PH and tiller number) were not detected in the late generations as they were due to dominance effects. Some of the identified QTLs co-mapped to well-known adaptive genes (i.e., Ppd-1, Vrn-1, and Rht-1). Other putative candidate genes were identified for each trait, of which PINE1 and PIF4 may be considered new for GH and TTN in wheat. The use of a large F2 mapping population combined with NGS-based genotyping techniques could improve map resolution and allow closer QTL tagging.

scholarly journals Crosses with spelt improve tolerance of South Asian spring wheat to spot blotch, terminal heat stress, and their combination

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ajeet Kumar Pandey ◽  
Vinod Kumar Mishra ◽  
Ramesh Chand ◽  
Sudhir Navathe ◽  
Neeraj Budhlakoti ◽  
...  
Keyword(s):  
Grain Yield ◽  
Spring Wheat ◽  
High Performance ◽  
Recombinant Inbred Lines ◽  
Spot Blotch ◽  
Spikelet Sterility ◽  
Strong Negative Correlation ◽  
Terminal Heat Stress ◽  
H 26 ◽  
The Individual

AbstractSpot blotch and terminal heat are two of the most important stresses for wheat in South Asia. A study was initiated to explore the use of spelt (Triticum spelta) to improve tolerance to these stresses in spring wheat (T. aestivum). We assessed 185 recombinant inbred lines (RILs) from the cross T. spelta (H + 26) × T. aestivum (cv. HUW234), under the individual stresses and their combination. H + 26 showed better tolerance to the single stresses and also their combination; grain yield in RILs was reduced by 21.9%, 27.7% and 39.0% under spot blotch, terminal heat and their combined effect, respectively. However, phenological and plant architectural traits were not affected by spot blotch itself. Multivariate analysis demonstrated a strong negative correlation between spikelet sterility and grain yield under spot blotch, terminal heat and their combination. However, four recombinant lines demonstrated high performance under both stresses and also under their combined stress. The four lines were significantly superior in grain yield and showed significantly lower AUDPC than the better parent. This study demonstrates the potential of spelt wheat in enhancing tolerance to spot blotch and terminal heat stresses. It also provides comprehensive evidence about the expression of yield and phenological traits under these stresses.

Spikelet fertility and heat shock transcription factor (Hsf) gene responses to heat stress in tolerant and susceptible rice (Oryza sativa L.) genotypes

2019 ◽  
Vol 157 (04) ◽  
pp. 283-299 ◽  
Author(s):  
C. Malumpong ◽  
S. Cheabu ◽  
C. Mongkolsiriwatana ◽  
W. Detpittayanan ◽  
A. Vanavichit
Keyword(s):  
Heat Stress ◽  
Pollen Germination ◽  
Seed Set ◽  
Oryza Sativa L ◽  
Flag Leaf ◽  
Pollen Viability ◽  
Spikelet Fertility ◽  
Anther Dehiscence ◽  
Spikelet Sterility ◽  
Plant Parts

AbstractThe reproductive stage of rice is the most sensitive to heat stress, which can lead to spikelet sterility. Thus, heat-tolerant and heat-susceptible genotypes were used to investigate their differences in terms of phenotypic responses and expression changes of Hsf genes at the pre-flowering stage under heat stress. Results clearly showed that panicles had the highest temperature compared with other plant parts under both natural and heated conditions. However, the temperatures of tolerant and susceptible genotypes were not significantly different. In terms of spikelet fertility, the tolerant lines M9962 and M7988 had high seed set because their anther dehiscence, pollen viability and pollen germination were only slightly affected. In contrast, the susceptible line Sinlek showed severe effects at all steps of fertilization, and the pollen viability of M7766 was slightly affected under heat stress but was more affected in terms of anther dehiscence and pollen germination. Both susceptible lines showed dramatically decreased seed set. In addition, the expression of six HsfA genes in the flag leaves and spikelets at the R2 stage of plants under heat stress showed different responses. Notably, expression of the HsfA2a gene was predominantly upregulated in the flag leaf and spikelets under heat stress in M9962. Therefore, it can be concluded that heat stress has severe effects on the stamen, and that different genotypes have different susceptibilities to heat stress.

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