Background
Unfavorable climatic changes have led to an increased threat of several biotic and abiotic stresses over the past few years. Looking at the massive damage caused by these stresses, we ...undertook a study to develop high yielding climate-resilient rice, using genes conferring resistance against blast (
Pi9
), bacterial leaf blight (BLB) (
Xa4, xa5, xa13, Xa21
), brown planthopper (BPH) (
Bph3, Bph17
), gall midge (GM) (
Gm4, Gm8
) and QTLs for drought tolerance (
qDTY
1.1
and
qDTY
3.1
) through marker-assisted forward breeding (MAFB) approach.
Result
Seven introgression lines (ILs) possessing a combination of seven to ten genes/QTLs for different biotic and abiotic stresses have been developed using marker-assisted selection (MAS) breeding method in the background of Swarna with drought QTLs. These ILs were superior to the respective recurrent parent in agronomic performance and also possess preferred grain quality with intermediate to high amylose content (AC) (23–26%). Out of these, three ILs viz., IL1 (
Pi9
+
Xa4
+
xa5
+
Xa21
+
Bph17
+
Gm8
+
qDTY
1.1
+
qDTY
3.1
), IL6 (
Pi9
+
Xa4
+
xa5
+
Xa21
+
Bph3
+
Bph17
+
Gm4
+
Gm8+ qDTY
1.1
+
qDTY
3.1
) and IL7 (
Pi9+ Xa4
+
xa5
+
Bph3
+
Gm4
+
qDTY
1.1
+
qDTY
3.1
) had shown resistance\tolerance for multiple biotic and abiotic stresses both in the field and glasshouse conditions. Overall, the ILs were high yielding under various stresses and importantly they also performed well in non-stress conditions without any yield penalty.
Conclusion
The current study clearly illustrated the success of MAS in combining tolerance to multiple biotic and abiotic stresses while maintaining higher yield potential and preferred grain quality. Developed ILs with seven to ten genes in the current study showed superiority to recurrent parent Swarna+drought for multiple-biotic stresses (blast, BLB, BPH and GM) together with yield advantages of 1.0 t ha
− 1
under drought condition, without adverse effect on grain quality traits under non-stress.
Characterization of physiological traits affected by rice breeding for grain yield under drought conditions shows that atmospheric and soil stresses strengthen the relationship between leaf traits ...and yield across extensive trials in South Asia.
Abstract
Direct selection for yield under drought has resulted in the release of a number of drought-tolerant rice varieties across Asia. In this study, we characterized the physiological traits that have been affected by this strategy in breeding trials across sites in Bangladesh, India, and Nepal. Drought- breeding lines and drought-tolerant varieties showed consistently longer flag leaves and lower stomatal density than our drought-susceptible check variety, IR64. The influence of environmental parameters other than drought treatments on leaf traits was evidenced by close grouping of treatments within a site. Flag-leaf length and width appeared to be regulated by different environmental parameters. In separate trials in the Philippines, the same breeding lines studied in South Asia showed that canopy temperature under drought and harvest index across treatments were most correlated with grain yield. Both atmospheric and soil stress strengthened the relationships between leaf traits and yield. The stable expression of leaf traits among genotypes and the identification of the environmental conditions in which they contribute to yield, as well as the observation that some breeding lines showed longer time to flowering and higher canopy temperature than IR64, suggest that selection for additional physiological traits may result in further improvements of this breeding pool.
Bacterial blight (BB) in rice caused by Xanthomonas oryzae pv. oryzae (Xoo) is a major global production constraint, particularly in irrigated and rain-fed lowland areas. Improved Samba Mahsuri (ISM) ...is an elite, high-yielding, fine-grain type, BB-resistant rice variety possessing three BB-resistant genes (Xa21, xa13 and xa5) and is highly popular in the southern parts of India. As the BB pathogen is highly dynamic and the evolution of pathogen virulence against the deployed resistance genes is common, we added a novel BB-resistant gene, Xa38, into ISM through marker-assisted backcross breeding (MABB) to increase the spectrum and durability of BB resistance. The breeding line PR 114 (Xa38) was used as the donor for Xa38, whereas ISM was used as the recurrent parent. Foreground selection was conducted using PCR-based gene-specific markers for the target genes, whereas background selection was conducted using a set of polymorphic SSR markers between the parents and backcrossing that continued until the third generation. Eighteen homozygous BC3F2 plants possessing all four BB-resistant genes in the homozygous state and with a recurrent parent genome (RPG) recovery of more than 92% were identified and advanced to the BC3F6 generation. These 18 backcross-derived lines (BDLs) exhibited very high level of resistance against multiple Xoo strains and displayed agro-morphological traits, grain qualities and yield levels similar to or better than those of the recurrent parent ISM.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The elite Indian rice variety, Naveen is highly susceptible to major biotic and abiotic stresses such as blast, bacterial blight (BB), gall midge (GM) and drought which limit its productivity in ...rainfed areas. In the present study, a combined approach of marker-assisted forward (MAFB) and back cross (MABC) breeding was followed to introgress three major genes, viz., Pi9 for blast, Xa21 for bacterial blight (BB), and Gm8 for gall midge (GM) and three major QTLs, viz., qDTY.sub.1.1, qDTY.sub.2.2 and qDTY.sub.4.1 conferring increased yield under drought in the background of Naveen. At each stage of advancement, gene-based/linked markers were used for the foreground selection of biotic and abiotic stress tolerant genes/QTLs. Intensive phenotype-based selections were performed in the field for identification of lines with high level of resistance against blast, BB, GM and drought tolerance without yield penalty under non-stress situation. A set of 8 MAFB lines and 12 MABC lines with 3 to 6 genes/QTLs and possessing resistance/tolerance against biotic stresses and reproductive stage drought stress with better yield performance compared to Naveen were developed. Lines developed through combined MAFB and MABC performed better than lines developed only through MAFB. This study exemplifies the utility of the combined approach of marker-assisted forward and backcrosses breeding for targeted improvement of multiple biotic and abiotic stress resistance in the background of popular mega varieties.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Lodging resistance in rice is a complex trait determined by culm morphological and culm physical strength traits, and these traits are a major determinant of yield. We made a detailed analysis of ...various component traits with the aim of deriving optimized parameters for measuring culm strength. Genotyping by sequencing (GBS)-based genome-wide association study (GWAS) was employed among 181 genotypes for dissecting the genetic control of culm strength traits. The VanRaden kinship algorithm using 6,822 filtered single-nucleotide polymorphisms (SNPs) revealed the presence of two sub-groups within the association panel with kinship values concentrated at<0.5 level, indicating greater diversity among the genotypes. A wide range of phenotypic variation and high heritability for culm strength and yield traits were observed over two seasons, as reflected in best linear unbiased prediction (BLUP) estimates. The multi-locus model for GWAS resulted in the identification of 15 highly significant associations (
< 0.0001) for culm strength traits. Two novel major effect marker-trait associations (MTAs) for section modulus and bending stress were identified on chromosomes 2 and 12 with a phenotypic variance of 21.87% and 10.14%, respectively. Other MTAs were also noted in the vicinity of previously reported putative candidate genes for lodging resistance, providing an opportunity for further research on the biochemical basis of culm strength. The quantitative trait locus (QTL) hotspot identified on chromosome 12 with the synergistic association for culm strength trait (section modulus, bending stress, and internode breaking weight) and grain number can be considered a novel genomic region that can serve a dual purpose of enhancing culm strength and grain yield. Elite donors in the
background with beneficial alleles of the identified major QTLs could be a valuable resource with greater significance in practical plant breeding programs focusing on improving lodging resistance in rice.
Advanced backcross introgression lines (BILs) developed from crosses of
var. Swarna/
accessions were grown and evaluated for yield and related traits. Trials were conducted for consecutive three ...seasons in field conditions in a randomized complete block design with three replications. Data on yield traits under irrigated conditions were analyzed using the Additive Main Effect and Multiplicative Interaction (AMMI), Genotype and Genotype × Environment Interaction (GGE) and modified rank-sum statistic (
) for yield stability. BILs
, G3 (14S) and G6 (166S) showed yield stability across the seasons along with high mean yield performance. G3 is early in flowering with high yield and has good grain quality and medium height, hence could be recommended for most of the irrigated locations. G6 is a late duration genotype, with strong culm strength, high grain number and panicle weight. G6 has higher yield and stability than Swarna but has Swarna grain type. Among the varieties tested DRRDhan 40 and recurrent parent Swarna showed stability for yield traits across the seasons. The component traits thousand grain weight, panicle weight, panicle length, grain number and plant height explained highest genotypic percentage over environment and interaction factors and can be prioritized to dissect stable QTLs/ genes. These lines were genotyped using microsatellite markers covering the entire rice genome and also using a set of markers linked to previously reported yield QTLs. It was observed that wild derived lines with more than 70% of recurrent parent genome were stable and showed enhanced yield levels compared to genotypes with higher donor genome introgressions.
Background
Climate extremes such as drought and flood have become major constraints to the sustainable rice crop productivity in rainfed environments. Availability of suitable climate-resilient ...varieties could help farmers to reduce the grain yield losses resulting from the climatic extremities. The present study was undertaken with an aim to develop high-yielding drought and submergence tolerant rice varieties using marker assisted introgression of
qDTY
1.1
,
qDTY
2.1
,
qDTY
3.1
and
Sub1.
Performance of near isogenic lines (NILs) developed in the background of Swarna was evaluated across 60 multi-locations trials (MLTs). The selected promising lines from MLTs were nominated and evaluated in national trials across 18 locations in India and 6 locations in Nepal.
Results
Grain yield advantage of the NILs with
qDTY
1.1
+ qDTY
2.1
+
qDTY
3.1
+
Sub1
and
qDTY
2.1
+
qDTY
3.1
+
Sub1
ranged from 76 to 2479 kg ha
− 1
and 396 to 2376 kg ha
− 1
under non-stress (NS) respectively and 292 to 1118 kg ha
− 1
and 284 to 2086 kg ha
− 1
under reproductive drought stress (RS), respectively. The NIL, IR96322–34-223-B-1-1-1-1 having
qDTY
1.1
+ qDTY
2.1
+
qDTY
3.1
+
Sub1
has been released as variety CR dhan 801 in India. IR 96321–1447-651-B-1-1-2 having
qDTY
1.1
+
qDTY
3.1
+
Sub 1
and IR 94391–131–358-19-B-1-1-1 having
qDTY
3.1
+
Sub1
have been released as varieties Bahuguni dhan-1′ and ‘Bahuguni dhan-2’ respectively in Nepal. Background recovery of 94%, 93% and 98% was observed for IR 96322–34-223-B-1-1-1-1, IR 96321–1447-651-B-1-1-2 and IR 94391–131–358-19-B-1-1-1 respectively on 6 K SNP Infinium chip.
Conclusion
The drought and submergence tolerant rice varieties with pyramided multiple QTLs can ensure 0.2 to 1.7 t ha
− 1
under reproductive stage drought stress and 0.1 to 1.0 t ha
− 1
under submergence conditions with no yield penalty under non-stress to farmers irrespective of occurrence of drought and/or flood in the same or different seasons.
Inter‐sub‐specific hybridization between indica and tropical japonica rice germplasm is the most efficient approach for broadening the genetic base of hybrid rice parental lines and enhancing the ...heterotic potential of hybrids in a tropical country like India. In the present study, 106 indica/tropical–japonica derived lines were developed through inter‐sub‐specific hybridization and screened using functional markers with respect to the major fertility restorer genes, Rf3 and Rf4, and the wide compatibility gene, S5n. The fertility restoration ability of newly developed restorers was validated through test cross nursery performance. The functional markers were observed to accurately predict the trait of fertility restoration. From the present study, the decreasing order of efficiency of different gene combinations on fertility restoration ability are as follows: Rf4/S5n > Rf4/Rf3/S5n > Rf4 > Rf4/Rf3 > Rf3/S5n > Rf3. Based on multi‐trait stability index (MTSI) analysis, the four newly identified restorers, that is, RP6388‐90, RP6382‐49, RP6375‐81 and RP6368‐38, were selected as the top best performing genotypes with high stability for multiple traits, and these genotypes will be useful for the development of superior rice hybrids in India.
The wild species of rice,
Oryza rufipogon
, is a source of genetic variation for yield-enhancing traits and blast resistance. With the objective to genetically enhance the elite rice cultivar, ‘Samba ...Mahsuri’, a set of 192 BC
2
F
2
and BC
2
F
3
lines developed from
O. rufipogon
was characterized for yield-enhancing traits and blast resistance. The study revealed the presence of significant genetic variability and transgressive segregation for productive tillers, spikelets per panicle, and grain yield per plant. The study also identified several introgression lines superior to the recurrent parent for yield enhancing traits and blast resistance. Molecular characterization of 26 blast resistant lines identified multiple blast resistance genes in IL-136
Pib
,
Pi
9 (t),
Pi54
,
Pi
38,
Pitp
and
Pi
20(t), IL-3
Pib
,
Pi54
,
Pi
38,
Pitp
and
Pi
20(t), and IL-140
Pib
,
Pi
9(t),
Pi54
,
Pi38
, and
Pitp
. Based on the performance of yield-enhancing traits and blast resistance, seven lines (IL-27, IL-28, IL-29, IL-72, IL-139, IL-158 and IL-171) showed merit. Estimation of the recovery of the recurrent parental genome by using 117 polymorphic SSR markers revealed that recurrent-parental genome recovery varied from 54.0 (IL-158) to 92.3% (IL-27). These promising, high-yielding introgression lines with multiple blast-resistance genes can serve as important genetic resources for yield and blast resistance improvement in rice, especially for the southern India.
Among the different challenges related to rice (Oryza sativa L.) cultivation, drought, bacterial leaf blight (BLB), and blast are the key stresses that significantly affect grain yield (GY) in rice. ...To ameliorate this issue, marker‐assisted forward breeding (MAFB) coupled with a simultaneous crossing approach was used to combine three drought tolerant quantitative trait loci (QTL)—qDTY1.1, qDTY3.1, and qDTY12.1—four BLB genes—Xa4, xa5, xa13, and Xa21—and one blast‐resistance gene, Pi9, in the elite rice cultivar Lalat. The introgression lines (ILs) developed in the current study were phenotypically screened for drought, BLB, and blast resistance at the F7–F8 generation. Under the reproductive stage (RS) drought stress, the yield advantage of ILs, with major‐effect QTL (qDTY) over elite parent Lalat, ranges from 9 to 124% in DS2019 and from 7 to 175% in WS2019. The selected ILs were highly resistant to BLB, with lesion lengths ranging from 1.3 to 3.0 cm and blast scores ranging from 1 to 3. ILs that were tolerant to RS drought, resistant to BLB, and blast disease and had similar or higher yields than Lalat were analyzed for grain quality. Six ILs were found to have similar grain quality characteristics to Lalat including hulling, milling, head rice recovery (HRR), chalkiness, alkali spreading value (ASV), and amylose content (AC). This study showed that MAFB, together with simultaneous crossing, would be an effective strategy to rapidly combine multiple stresses in rice. The ILs developed in this study could help to ensure yield sustainability in rainfed environments or be used as genetic material in future breeding programs.
Core Ideas
Changing climatic conditions have increased the occurrence of various stresses in rice.
Marker‐assisted forward breeding is a quick and effective method for combining multiple QTL and genes.
Lines with 5–8 QTL and genes for drought and genes for blast and bacterial leaf blight were developed.
Lines having multiple QTL and genes reduce yield loss caused by different stresses.
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