Genetic Gains of Full-Sib Families from Disconnected Diallels in Loblolly Pine

Abstract Breeding values for the 2nd-cycle of the loblolly pine (Pinus taeda L.) breeding program were analyzed with the NCSUIndustry Tree Improvement Cooperative database to estimate genetic gains and compare different strategies for full-sib deployment. In the disconnected half-diallel mating design used for loblolly pine, six parents within each diallel were crossed to generate 15 full-sib families for general combining ability (GCA) and specific combining ability (SCA) estimates. Parents among disconnected diallels were never crossed, and the SCA and full-sib family breeding values cannot be estimated directly. Using the GCA and SCA estimates from 60 diallels in the Atlantic Coastal region of loblolly pine, genetic gains were estimated in this study for full-sib families within the disconnected diallels and then compared with the potential gains that would be expected if we select parents for full-sib families based on GCA values for all parents within a geographic region. As the dominance variance was found to be much less than the additive variance, the SCA contribution to the full-sib genetic gain was relatively small. Higher full-sib genetic gains were obtained by crossing the best GCA parents from different diallels within a geographic region than selecting only those within diallels. The difference increased with increasing number of selected full-sibs. Results from different selection scenarios, with various selection intensities and relatedness managements, suggest that selection based on GCA from all parents within a geographic region would result in a higher genetic gain for full-sib families in loblolly pine. The deployment of full-sib families are very important for achieving higher genetic gains in a loblolly pine breeding program. But they were not due to the SCA contribution, but rather due to high GCA of best parents in creating these full-sib crosses. The strategies for family and clonal deployment are very attractive based on the data from this study.

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Genetic Trends Estimation in IRRIs Rice Drought Breeding Program and Identification of High Yielding Drought-Tolerant Lines

10.21203/rs.3.rs-910539/v1 ◽

2021 ◽

Author(s):

Apurva Khanna ◽

Mahender Anumalla ◽

Margaret Catolos ◽

Jérôme Bartholomé ◽

Roberto Fritsche-Neto ◽

...

Keyword(s):

Grain Yield ◽

Genetic Gain ◽

Recurrent Selection ◽

Historical Data ◽

Breeding Program ◽

Positive Trend ◽

Breeding Values ◽

Genetic Gains ◽

Rate Of Increase ◽

Genetic Trends

Abstract BackgroundEstimation of genetic trends using historical data is an important parameter to check the success of the breeding programs. The estimated genetic trends can act as a guideline to target the appropriate breeding strategies and optimize the breeding program for improved genetic gains. In this study, 17 years of historical data from IRRI’s rice drought breeding program was used to estimate the genetic trends and assess the success of the breeding program. We also identified top-performing lines based on grain yield breeding values as an elite panel for implementing future population improvement-based breeding schemes.ResultsA two-stage approach of pedigree-based mixed model analysis was used to analyze the data and extract the breeding values and estimate the genetic trends for grain yield under non-stress, drought, and in combined data of non-stress and drought. Lower grain yield values were observed in all the drought trials. Heritability for grain yield estimates ranged between 0.20-0.94 under the drought trials, and 0.43-0.83 under non-stress trials. Under non-stress conditions the genetic gain of 0.44% (21.20 kg/ha/year) for genotypes and 0.17 % (7.90 kg/ha/year) for checks was observed. The genetic trend under the drought conditions exhibited a positive trend with the genetic gain of 0.11% (1.98kg/ha/year) for genotypes and 0.55% (9.52kg/ha/year) for checks. For combined analysis showed a genetic gain of 0.39% (12.13 kg/ha/year) for genotypes and 0.60% (13.69 kg/ha/year) for checks was observed. For elite panel selection, 200 promising lines were selected based on higher breeding values for grain yield and prediction accuracy of >0.40. The breeding values of the 200 genotypes formulating the core panel ranged between 2366.17 and 4622.59 (kg/ha).ConclusionsA positive genetic rate was observed under all the three conditions; however, the rate of increase was lower than the required rate of 1.5% genetic gain. We propose a recurrent selection breeding strategy within the elite population with the integration of modern tools and technologies to boost the genetic gains in IRRI’s drought breeding program. The elite breeding panel identified in this study forms an easily available and highly enriched genetic resource for future recurrent selection programs to boost the genetic gains.

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Inheritance of Physico-chemical Seed Characters Related to Culinary Quality in Dry Bean

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.115.3.492 ◽

1990 ◽

Vol 115 (3) ◽

pp. 492-499 ◽

Cited By ~ 16

Author(s):

N.N. Wassimi ◽

G.L. Hosfield ◽

M.A. Uebersax

Keyword(s):

Combining Ability ◽

Recurrent Selection ◽

Weight Coefficient ◽

Additive Variance ◽

Dry Bean ◽

Mean Values ◽

Culinary Quality ◽

Physico Chemical ◽

Diallel Mating Design ◽

San Fernando

Culinary quality in dry bean (Phaseolus vulgaris L.) depends on attributes of seeds prevailing at harvest and is determined by the genetic architecture of cultivars and by unpredictable environmental factors. Variation among genotypes for culinary quality has been shown to be heritable; however, the efficacy of selection depends on a knowledge of the genetic control of the measured traits. A diallel mating design was used to estimate the combining ability of parents and determine the inheritance of nine culinary quality traits important to processors and consumers. Genetic variability among eight parents, 56 F2, and 56 F3 progenies was confirmed by significant mean squares from analyses of variance. Significant variability detected between F2 and F3 progenies for soaked bean weight (SBWT), soaked bean water content (SBWC), and clumps (CLMP) was due to inbreeding effects. General combining ability (GCA) components were highly significant and overshadowed specific combining ability (SCA) components in the F2 and F3 for SBWT, SBWC, split beans (SPLT), and the washed-drained weight coefficient (WDWTR), indicating that additive variance predominated. Ratios of GCA: SCA components were equal to or less than unity for CLMP, washed-drained weight (WDWT), and texture (TEXT), indicating that both additive and nonadditive effects contributed to trait expression. Significant SCA effect variances were noted for `Sanilac', `San Fernando', `Nep-2', and `A-30' for WDWT and TEXT, implying that progeny from crosses of these parents had higher or lower mean values for the traits titan the average expected on the basis of GCA. Graphs of the regression of Vr on Wr showed that genes controlling WDWT and TEXT were completely dominant in most cases. Recurrent selection, which seeks to concentrate favorable alleles with additive effects in populations, may he an effective breeding procedure to improve the culinary quality of dry beans. It is not feasible to breed for TEXT and WDWT simultaneously because of a negative correlation between the traits.

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Combining Ability for Resistance to Sweetpotato Feathery Mottle Virus

HortScience ◽

10.21273/hortsci.35.7.1319 ◽

2000 ◽

Vol 35 (7) ◽

pp. 1319-1320 ◽

Cited By ~ 9

Author(s):

Elisa Mihovilovich ◽

Humberto A. Mendoza ◽

Luis F. Salazar

Keyword(s):

Combining Ability ◽

Ipomoea Batatas ◽

Block Design ◽

Mottle Virus ◽

Combining Abilities ◽

Diallel Mating Design ◽

Additive Gene ◽

Sib Families ◽

Design Resistance ◽

Selection Of

Combining ability for resistance to Sweetpotato Feathery Mottle Virus (SPFMV) was evaluated in seven sweetpotato [Ipomoea batatas (L.) Lam] clones. A diallel mating design was used, which resulted in 16 full-sib families. Families were evaluated for SPFMV resistance under greenhouse conditions in a randomized complete-block design. Resistance was tested by grafting Ipomoea nil `Scarlet O' Hara' infected with the russet crack strain of SPFMV (RC-SPFMV) onto individual plants of the families being evaluated. Symptomless plants were further indexed by cleft grafting virus-free Ipomoea setosa Ker plants onto the tested plants. Those plants in which the virus was not recovered by this test were considered resistant. Analysis of variance for SPFMV resistance revealed significant general combining abilities (GCA). Two clones, DLP-886 and TN90.300, exhibited significant positive GCA for SPFMV resistance. No significant specific combining abilities (SCA) were detected among the crosses. Breeding for resistance to SPFMV should focus on careful selection of resistant parents. In addition, results suggest that additive gene action is important in resistance to SPFMV.

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Identification of an Elite Core Panel as a Key Breeding Resource to Accelerate the Rate of Genetic Improvement for Irrigated Rice

10.21203/rs.3.rs-832443/v1 ◽

2021 ◽

Author(s):

Roselyne U. Juma ◽

Jérôme Bartholomé ◽

Parthiban Thathapalli Prakash ◽

Waseem Hussain ◽

John Damien Platten ◽

...

Keyword(s):

Grain Yield ◽

Genetic Gain ◽

Genetic Improvement ◽

Critical Role ◽

The Philippines ◽

Breeding Program ◽

Breeding Cycle ◽

Relationship Matrix ◽

Irrigated Rice ◽

Breeding Values

Abstract Rice genetic improvement is a key component of achieving and maintaining food security in Asia and Africa in the face of growing populations and climate change. In this effort, the International Rice Research Institute (IRRI) continues to play a critical role in creating and disseminating rice varieties with higher productivity. Due to increasing demand for rice, especially in Africa, there is a strong need to accelerate the rate of genetic improvement for grain yield.In an effort to identify and characterize the elite breeding pool of IRRI’s irrigated rice breeding program, we analyzed 102 historical yield trials conducted in the Philippines during the period 2012-2016 and representing 15,286 breeding lines (including released varieties). A mixed model approach based on the pedigree relationship matrix was used to estimate breeding values for grain yield, which ranged from 2.12 to 6.27 t·ha-1. The rate of genetic gain for grain yield was estimated at 8.75 kg·ha-1·year-1 (0.23%) for crosses made in the period from 1964 to 2014. Reducing the data to only IRRI released varieties, the rate doubled to 17.36 kg·ha-1·year-1 (0.46%). Regressed against breeding cycle the rate of gain for grain yield was 185 kg·ha-1·cycle-1 (4.95%). We selected 72 top performing lines based on breeding values for grain yield to create an elite core panel (ECP) representing the genetic diversity in the breeding program with the highest heritable yield values from which new products can be derived. The ECP closely aligns with the indica 1B sub-group of Oryza sativa that includes most modern varieties for irrigated systems. Agronomic performance of the ECP under multiple environments in Asia and Africa confirmed its high yield potential.We found that the rate of genetic gain for grain yield found in this study was limited primarily by long cycle times and the direct introduction of non-improved material into the elite pool. Consequently, the current breeding scheme for irrigated rice at IRRI is based on rapid recurrent selection among highly elite lines. In this context, the ECP constitutes an important resource for IRRI and NAREs breeders to carefully characterize and manage that elite diversity.

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Inheritance of Resistance to Colletotrichum gloeosporioides and C. acutatum in Strawberry

Phytopathology ◽

10.1094/phyto-08-18-0283-r ◽

2019 ◽

Vol 109 (3) ◽

pp. 428-435 ◽

Cited By ~ 2

Author(s):

Raymond L. Jacobs ◽

Tika B. Adhikari ◽

Jeremy Pattison ◽

G. Craig Yencho ◽

Gina E. Fernandez ◽

...

Keyword(s):

Genetic Control ◽

Colletotrichum Gloeosporioides ◽

Leaf Tissue ◽

Crown Rot ◽

Valuable Insight ◽

Inheritance Of Resistance ◽

Additive Variance ◽

Diallel Mating Design ◽

Crown Tissue ◽

Sib Families

Information on the inheritance of resistance to Colletotrichum gloeosporioides and C. acutatum hemibiotrophic infections (HBI) in strawberry leaf tissue and the genetic control of anthracnose crown rot (ACR) in crown tissue are relatively unknown. Six parental genotypes were crossed in a half-diallel mating design to generate 15 full-sib families. HBI and ACR experiments were conducted concurrently. Both seedlings and parental clones were inoculated with 1 × 106 conidia/ml of C. gloeosporioides or C. acutatum. Percent sporulating leaf area, wilt symptoms, and relative area under the disease progress curve were calculated to characterize resistance among genotypes and full-sib families. Low dominance/additive variance ratios for C. acutatum HBI (0.13) and C. gloeosporioides ACR (0.20) were observed, indicating additive genetic control of resistance to these traits. Heritability estimates were low for C. acutatum HBI (0.25) and C. gloeosporioides HBI (0.16) but moderate for C. gloeosporioides ACR (0.61). A high genetic correlation (rA = 0.98) between resistance to C. acutatum HBI and C. gloeosporioides HBI was observed, suggesting that resistance to these two Colletotrichum spp. may be controlled by common genes in strawberry leaf tissue. In contrast, negative genetic correlations between ACR and both HBI traits (rA = −0.85 and −0.61) suggest that resistance in crown tissue is inherited independently of resistance in leaf tissue in the populations tested. Overall, these findings provide valuable insight into the genetic basis of resistance, and the evaluation and deployment of resistance to HBIs and ACR in strawberry breeding programs.

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Genetic Variation and Gains in Resistance of Strawberry to Colletotrichum gloeosporioides

Phytopathology ◽

10.1094/phyto-02-13-0032-r ◽

2014 ◽

Vol 104 (1) ◽

pp. 67-74 ◽

Cited By ~ 12

Author(s):

L. F. Osorio ◽

J. A. Pattison ◽

N. A. Peres ◽

V. M. Whitaker

Keyword(s):

North Carolina ◽

Genetic Variation ◽

Genetic Control ◽

Colletotrichum Gloeosporioides ◽

Crown Rot ◽

Additive Variance ◽

Resistant Parent ◽

Genetic Gains ◽

The North ◽

Diallel Mating Design

Anthracnose crown rot is an important disease of strawberry primarily caused by Colletotrichum gloeosporioides in Florida and North Carolina. Information on the magnitude of additive and nonadditive genetic variation is required to define breeding strategies and to estimate potential genetic gains. However, little is known about the genetic control of resistance and its utility in breeding. Our objectives were to obtain estimates of heritabilities and of components of genetic variances, genotype–environment interactions, and gains for resistance, and to examine the effects of locations and transplant types on the estimates. An incomplete diallel mating design generated 42 full-sib families, which were propagated in plugs from seed (seedling tests) and as bare-root runner plants (clonal tests) of different genotypes of the same families. Both seedlings and clones were inoculated with C. gloeosporioides under field conditions in North Carolina and Florida during the 2010–11 season. Narrow-sense heritability (h2) and broad-sense heritability (H2) for both clones and seedlings were higher at the North Carolina location (h2 = 0.34 to 0.62 and H2 = 0.46 to 0.85) than at the Florida location (h2 = 0.16 to 0.22 and H2 = 0.37 to 0.46). Likewise, the seedling tests showed higher genetic control than the clonal tests at both locations. Estimates of dominance variance were approximately one-third of the additive variance at North Carolina and were even larger at Florida. Epistasis was negative at both locations and assumed zero for heritability (H2) calculations. Genotype–environment interactions were different by transplant type, suggesting rank changes across locations. ‘Pelican’ was the most resistant parent at both locations, followed by ‘NCH09-68’ at the NC location and ‘Winter Dawn’ at the Florida location. Selection and deployment of the most resistant clone within each of the five best families is estimated to produce average genetic gains of 53.0 and 73.7% at the North Carolina and Florida locations, respectively.

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Predicted genetic gains and testing efficiency from two loblolly pine clonal trials

Canadian Journal of Forest Research ◽

10.1139/x05-064 ◽

2005 ◽

Vol 35 (7) ◽

pp. 1754-1766 ◽

Cited By ~ 23

Author(s):

Fikret Isik ◽

Barry Goldfarb ◽

Anthony LeBude ◽

Bailian Li ◽

Steve McKeand

Keyword(s):

South Carolina ◽

Loblolly Pine ◽

Growth Traits ◽

Field Trials ◽

Clonal Forestry ◽

Fusiform Rust ◽

Genetic Gains ◽

Rust Infection ◽

Volume Yield ◽

Sib Families

Clonal field trials were established at two sites using rooted cuttings from 450 clones of eight full-sib families of loblolly pine (Pinus taeda L.). Height, survival, fusiform rust infection (caused by Cronartium quercuum (Berk) Miyabe ex Shirai f.sp. fusiforme), bole straightness, and diameter were measured after four growing seasons. There were significant differences among full-sib families and among clones within families for all traits studied. Moderately high within-family repeatabilities of clone means (0.50 to 0.75) for growth traits and a very high within-family repeatability of clone means (0.94) for fusiform rust infection were estimated. When the best eight clones were selected regardless of family structure, the volume yield was 52% greater than that of the unimproved seedlings at two sites. Selection of the best two clones from each of four families produced only slightly lower estimated genetic gains than the above scenario. The probability of fusiform rust infection ranged from 0.08 to 0.93 among clones at the South Carolina site. Predicted genetic gain for rust resistance was relatively insensitive to selection intensity, as there were numerous clones with high apparent resistance. The number of ramets per clone necessary to reliably characterize performance on one site was estimated to be between four and six. These results contribute to estimates of the gains available from clonal forestry and will help guide clonal testing and selection programs. Implementation of clonal forestry and cost issues are discussed.

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Combining Ability Analysis in 10 Strawberry Genotypes Used in Breeding Cultivars for Tolerance to Verticillium Wilt

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.139.3.275 ◽

2014 ◽

Vol 139 (3) ◽

pp. 275-281 ◽

Cited By ~ 3

Author(s):

Agnieszka Masny ◽

Edward Żurawicz ◽

Kris Pruski ◽

Wiesław Mądry

Keyword(s):

Verticillium Wilt ◽

Combining Ability ◽

Field Experiments ◽

Genetic Transmission ◽

Diallel Mating Design ◽

Combining Ability Analysis ◽

Sib Families ◽

Strawberry Breeding ◽

Half Diallel ◽

Made In

General combining ability (GCA) and specific combining ability (SCA) effects of 10 strawberry (Fragaria ×ananassa) cultivars (Darselect, Selvik, Elianny, Figaro, Sonata, Susy, Salsa, Albion, Charlotte, and Filon) for severity of verticillium wilt (Verticillium dahliae) were estimated. Progeny consisting of 45 F1 full-sib families from the crosses made in a half diallel mating design according to the IV Griffing’s method was evaluated in two field experiments conducted in 2009 and 2010 on a soil heavily infested with V. dahliae inoculum. Each hybrid family was represented by 60 seedlings (four replicates of 15 plants each). The analysis of variance revealed significant (P < 0.01) GCA and SCA effects of the parental cultivars for the verticillium wilt severity in plants. This suggests that genetic additive and non-additive effects are involved in the inheritance of strawberry tolerance to verticillium wilt. In 2009, a significant negative GCA effect (P < 0.05) for the verticillium wilt severity in plants was found in ‘Selvik’, ‘Filon’, and ‘Sonata’, indicating genetic transmission of tolerance from parents to the offspring. On the other hand, a significant (P < 0.05) and positive for the verticillium wilt severity GCA effect was found for ‘Figaro’ in 2009, indicating the transmission from this parent to its offspring relatively high susceptibility to the wilt. Only in one hybrid family, ‘Albion’ × ‘Charlotte’, was the SCA effect significantly positive (P < 0.05) for verticillium wilt severity in plants, whereas two other hybrid families—‘Selvik’ × ‘Salsa’ and ‘Sonata’ × ‘Albion’—showed significantly negative SCA effects (P < 0.05). Three of 10 evaluated genotypes (i.e., ‘Selvik’, ‘Filon’, and ‘Sonata’) were found to be the most valuable parents to the strawberry breeding program for tolerance to verticillium wilt. The least suitable cultivar for this purpose was ‘Figaro’.

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Simulation studies to optimize genomic selection in honey bees

Genetics Selection Evolution ◽

10.1186/s12711-021-00654-x ◽

2021 ◽

Vol 53 (1) ◽

Author(s):

Richard Bernstein ◽

Manuel Du ◽

Andreas Hoppe ◽

Kaspar Bienefeld

Keyword(s):

Genomic Selection ◽

Genetic Gain ◽

Honey Bees ◽

Reference Population ◽

Breeding Program ◽

Genomic Relationship Matrix ◽

Relationship Matrix ◽

Genomic Relationship ◽

Genomic Breeding ◽

Breeding Values

Abstract Background With the completion of a single nucleotide polymorphism (SNP) chip for honey bees, the technical basis of genomic selection is laid. However, for its application in practice, methods to estimate genomic breeding values need to be adapted to the specificities of the genetics and breeding infrastructure of this species. Drone-producing queens (DPQ) are used for mating control, and usually, they head non-phenotyped colonies that will be placed on mating stations. Breeding queens (BQ) head colonies that are intended to be phenotyped and used to produce new queens. Our aim was to evaluate different breeding program designs for the initiation of genomic selection in honey bees. Methods Stochastic simulations were conducted to evaluate the quality of the estimated breeding values. We developed a variation of the genomic relationship matrix to include genotypes of DPQ and tested different sizes of the reference population. The results were used to estimate genetic gain in the initial selection cycle of a genomic breeding program. This program was run over six years, and different numbers of genotyped queens per year were considered. Resources could be allocated to increase the reference population, or to perform genomic preselection of BQ and/or DPQ. Results Including the genotypes of 5000 phenotyped BQ increased the accuracy of predictions of breeding values by up to 173%, depending on the size of the reference population and the trait considered. To initiate a breeding program, genotyping a minimum number of 1000 queens per year is required. In this case, genetic gain was highest when genomic preselection of DPQ was coupled with the genotyping of 10–20% of the phenotyped BQ. For maximum genetic gain per used genotype, more than 2500 genotyped queens per year and preselection of all BQ and DPQ are required. Conclusions This study shows that the first priority in a breeding program is to genotype phenotyped BQ to obtain a sufficiently large reference population, which allows successful genomic preselection of queens. To maximize genetic gain, DPQ should be preselected, and their genotypes included in the genomic relationship matrix. We suggest, that the developed methods for genomic prediction are suitable for implementation in genomic honey bee breeding programs.

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Identification of an Elite Core Panel as a Key Breeding Resource to Accelerate the Rate of Genetic Improvement for Irrigated Rice

Rice ◽

10.1186/s12284-021-00533-5 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Roselyne U. Juma ◽

Jérôme Bartholomé ◽

Parthiban Thathapalli Prakash ◽

Waseem Hussain ◽

John D. Platten ◽

...

Keyword(s):

Grain Yield ◽

Genetic Gain ◽

Genetic Improvement ◽

Critical Role ◽

The Philippines ◽

Breeding Program ◽

Yield Potential ◽

Relationship Matrix ◽

Irrigated Rice ◽

Breeding Values

AbstractRice genetic improvement is a key component of achieving and maintaining food security in Asia and Africa in the face of growing populations and climate change. In this effort, the International Rice Research Institute (IRRI) continues to play a critical role in creating and disseminating rice varieties with higher productivity. Due to increasing demand for rice, especially in Africa, there is a strong need to accelerate the rate of genetic improvement for grain yield. In an effort to identify and characterize the elite breeding pool of IRRI’s irrigated rice breeding program, we analyzed 102 historical yield trials conducted in the Philippines during the period 2012–2016 and representing 15,286 breeding lines (including released varieties). A mixed model approach based on the pedigree relationship matrix was used to estimate breeding values for grain yield, which ranged from 2.12 to 6.27 t·ha−1. The rate of genetic gain for grain yield was estimated at 8.75 kg·ha−1 year−1 (0.23%) for crosses made in the period from 1964 to 2014. Reducing the data to only IRRI released varieties, the rate doubled to 17.36 kg·ha−1 year−1 (0.46%). Regressed against breeding cycle the rate of gain for grain yield was 185 kg·ha−1 cycle−1 (4.95%). We selected 72 top performing lines based on breeding values for grain yield to create an elite core panel (ECP) representing the genetic diversity in the breeding program with the highest heritable yield values from which new products can be derived. The ECP closely aligns with the indica 1B sub-group of Oryza sativa that includes most modern varieties for irrigated systems. Agronomic performance of the ECP under multiple environments in Asia and Africa confirmed its high yield potential. We found that the rate of genetic gain for grain yield found in this study was limited primarily by long cycle times and the direct introduction of non-improved material into the elite pool. Consequently, the current breeding scheme for irrigated rice at IRRI is based on rapid recurrent selection among highly elite lines. In this context, the ECP constitutes an important resource for IRRI and NAREs breeders to carefully characterize and manage that elite diversity.

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