General combining ability of most yield-related traits had a genetic basis different from their corresponding traits per se in a set of maize introgression lines

Genetic Dissection of the General Combining Ability of Yield-Related Traits in Maize

Maize yield components including row number, kernel number per row, kernel thickness, kernel width, kernel length, 100-kernel weight, and volume weight affect grain yield directly. Previous studies mainly focused on dissecting the genetic basis of per se performances for yield-related traits, but the genetic basis of general combining ability (GCA) for these traits is still unclear. In the present study, 328 RILs were crossed as males to two testers according to the NCII mating design, resulting in a hybrid panel composed of 656 hybrids. Both the hybrids and parental lines were evaluated in four environments in 2015 and 2016. Correlation analysis showed the performances of GCA effects were significantly correlated to the per se performances of RILs for all yield-related traits (0.17 ≤ r ≤ 0.64, P > 0.01). Only 17 of 95 QTL could be detected for both per se performances of RILs and GCA effects for eight yield-related traits. The QTL qKN7-1 and qHKW1-3, which could explain more than 10% of the variation in the GCA effects of KN and HKW, were also detected for per se performances for the traits. The pleiotropic loci qRN3-1 and qRN6, which together explained 14.92% of the observed variation in GCA effects for RN, were associated with the GCA effects of KW and HKW, but not with per se performances for these traits. In contrast, Incw1, which was related to seed weight in maize, was mapped to the region surrounding MK2567 at the qHKW5-2 locus, but no GCA effect was detected. The QTL identified in present study for per se performances and corresponding GCA effects for yield-related traits might be useful for maize hybrid breeding.

Association analysis between constructed SNPLDBs and GCA effects of 9 quality-related traits in parents of hybrid rice (Oryza sativa L.)

BACKGROUND

The general combining ability (GCA) of parents in hybrid rice affects not only heterotic level of grain yield and other important agronomic traits, but also performance of grain quality traits of F₂ bulk population which is the commodity consumed by humans. In order to make GCA improvement for quality traits in parents of hybrid rice by molecular marker assisted selection feasible, genome-wide GCA loci for quality traits in parents were detected through association analysis between the effects of GCA and constructed single nucleotide polymorphism linkage disequilibrium blocks (SNPLDBs), by using unhusked rice grains harvested from F₁ plants of 48 crosses of Indica rice and 78 crosses of Japonica rice. GCA-SNPLDBs association analysis.

RESULTS

Among the 8 CMS and 6 restorer lines of indica rice subspecies, CMS lines Zhenpin A, Zhenshan97 A, and 257A, and restorers Kanghui98, Minghui63 and Yanhui559 were recognized as good general combiners based on their GCA effect values for the 9 quality traits (brown rice rate, milled rice rate, head rice rate, percentage of chalky grains, chalky area size, chalkiness degree, gelatinization temperature, gel consistency and amylose content). Among the 13 CMS and 6 restorer lines of japonica rice subspecies, CMS 863A, 6427A and Xu 2A, and restorers C418, Ninghui8hao and Yunhui4hao showed elite GCA effect values for the 9 traits. GCA-SNPLDB association analysis revealed 39 significant SNPLDB loci associated with the GCA of the 9 quality-related traits, and the numbers of SNPLDB loci located on chromosome 1, 2, 3, 4, 5, 8, 9, 11 and 12 were 1, 4, 3, 9, 6, 5, 5, 4 and 2, respectively. Number of superior GCA alleles for the 9 traits among the 33 parents ranged from 1 to 26.

CONCLUSIONS

Thirty-nine significant SNPLDBs loci were identified associated with the GCA of 9 quality-related traits, and the superior SNPLDB alleles could be used to improve the GCA of parents for the traits in the future by molecular marker assisted selection. The genetic basis of trait GCA in parents is different from that of trait itself.

B. K, Satyavathi CT, Kumar S, Singh RB, Yadav RS, Gupta R, Srivastava RK. Discerning combining ability loci for divergent environments using chromosome segment substitution lines (CSSLs) in pearl millet

Pearl millet is an important crop for arid and semi-arid regions of the world. Genomic regions associated with combining ability for yield-related traits under irrigated and drought conditions are useful in heterosis breeding programs. Chromosome segment substitution lines (CSSLs) are excellent genetic resources for precise QTL mapping and identifying naturally occurring favorable alleles. In the present study, testcross hybrid populations of 85 CSSLs were evaluated for 15 grain and stover yield-related traits for summer and wet seasons under irrigated control (CN) and moisture stress (MS) conditions. General combining ability (GCA) and specific combining ability (SCA) effects of all these traits were estimated and significant marker loci linked to GCA and SCA of the traits were identified. Heritability of the traits ranged from 53-94% in CN and 63-94% in MS. A total of 40 significant GCA loci and 36 significant SCA loci were identified for 14 different traits. Five QTLs (flowering time, panicle number and panicle yield linked to Xpsmp716 on LG4, flowering time and grain number per panicle with Xpsmp2076 on LG4) simultaneously controlled both GCA and SCA, demonstrating their unique genetic basis and usefulness for hybrid breeding programs. This study for the first time demonstrated the potential of a set of CSSLs for trait mapping in pearl millet. The novel combining ability loci linked with GCA and SCA values of the traits identified in this study may be useful in pearl millet hybrid and population improvement programs using marker-assisted selection (MAS).

Genome-Wide Single-Nucleotide Polymorphisms in CMS and Restorer Lines Discovered by Genotyping Using Sequencing and Association with Marker-Combining Ability for 12 Yield-Related Traits in Oryza sativa L. subsp. Japonica

Heterosis or hybrid vigor is closely related with general combing ability (GCA) of parents and special combining ability (SCA) of combinations. The evaluation of GCA and SCA facilitate selection of parents and combinations in heterosis breeding. In order to improve combining ability (CA) by molecular marker assist selection, it is necessary to identify marker loci associated with the CA. To identify the single nucleotide polymorphisms (SNP) loci associated with CA in the parental genomes of japonica rice, genome-wide discovered SNP loci were tested for association with the CA of 18 parents for 12 yield-related traits. In this study, 81 hybrids were created and evaluated to calculate the CA of 18 parents. The parents were sequenced by genotyping by sequencing (GBS) method for identification of genome-wide SNPs. The analysis of GBS indicated that the successful mapping of 9.86 × 10⁶ short reads in the Nipponbare reference genome consists of 39,001 SNPs in parental genomes at 11,085 chromosomal positions. The discovered SNPs were non-randomly distributed within and among the 12 chromosomes of rice. Overall, 20.4% (8026) of the discovered SNPs were coding types, and 8.6% (3344) and 9.9% (3951) of the SNPs revealed synonymous and non-synonymous changes, which provide valuable knowledge about the underlying performance of the parents. Furthermore, the associations between SNPs and CA indicated that 362 SNP loci were significantly related to the CA of 12 parental traits. The identified SNP loci of CA in our study were distributed genome wide and caused a positive or negative effect on the CA of traits. For the yield-related traits, such as grain thickness, days to heading, panicle length, grain length and 1000-grain weight, a maximum number of positive SNP loci of CA were found in CMS A171 and in the restorers LC64 and LR27. On an individual basis, some of associated loci that resided on chromosomes 2, 5, 7, 9, and 11 recorded maximum positive values for the CA of traits. From our results, we suggest that heterosis in japonica rice would be improved by pyramiding the favorable SNP loci of CA and eliminating the unfavorable loci from parental genomes.

Breeding signature of combining ability improvement revealed by a genomic variation map from recurrent selection population in Brassica napus

Combining ability is crucial for parent selection in crop hybrid breeding. The present investigation and results had revealed the underlying genetic factors which might contribute in adequate combining ability, further assisting in enhancing heterosis and stability. Here, we conducted a large-scale analysis of genomic variation in order to define genomic regions affecting the combining ability in recurrent selection population of rapeseed. A population of 175 individuals was genotyped with the Brassica60K SNP chip. 525 hybrids were assembled with three different testers and used to evaluate the general combining ability (GCA) in three environments. By detecting the changes of the genomic variation, we identified 376 potential genome regions, spanning 3.03% of rapeseed genome which provided QTL-level resolution on potentially selected variants. More than 96% of these regions were located in the C subgenome, indicating that C subgenome had sustained stronger selection pressure in the breeding program than the A subgenome. In addition, a high level of linkage disequilibrium in rapeseed genome was detected, suggesting that marker-assisted selection for the population improvement might be easily implemented. This study outlines the evidence for high GCA on a genomic level and provided underlying molecular mechanism for recurrent selection improvement in B. napus.

Genetic Analysis in Maize Foundation Parents with Mapping Population and Testcross Population: Ye478 Carried More Favorable Alleles and Using QTL Information Could Improve Foundation Parents

The development of maize foundation parents is an important part of genetics and breeding research, and applying new genetic information to produce foundation parents has been challenging. In this study, we focused on quantitative trait loci (QTLs) and general combining ability (GCA) of Ye478, a widely used foundation parent in China. We developed three sets of populations for QTL mapping and to analyze the GCA for some agronomic traits. The assessment of 15 traits resulted in the detection of 251 QTLs in six tested environments, with 119 QTLs identified through a joint analysis across all environments. Further, analyses revealed that most favorable alleles for plant type-related traits were from Ye478, and more than half of the favorable alleles for yield-related traits were from R08, another foundation parent used in southwestern China, suggesting that different types of foundation parents carried different favorable alleles. We observed that the GCA for most traits (e.g., plant height and 100-kernel weight) was maintained in the inbred lines descended from the foundation parents. Additionally, the continuous improvement in the GCA of the descendants of the foundation parents was consistent with the main trend in maize breeding programs. We identified three significant genomic regions that were highly conserved in three Ye478 descendants, including the stable QTL for plant height. The GCA for the traits in the F₇ generation revealed that the QTLs for the given traits per se were affected by additive effects in the same way in different populations.

Genetic dissection of heterosis using epistatic association mapping in a partial NCII mating design

Heterosis refers to the phenomenon in which an F₁ hybrid exhibits enhanced growth or agronomic performance. However, previous theoretical studies on heterosis have been based on bi-parental segregating populations instead of F₁ hybrids. To understand the genetic basis of heterosis, here we used a subset of F₁ hybrids, named a partial North Carolina II design, to perform association mapping for dependent variables: original trait value, general combining ability (GCA), specific combining ability (SCA) and mid-parental heterosis (MPH). Our models jointly fitted all the additive, dominance and epistatic effects. The analyses resulted in several important findings: 1) Main components are additive and additive-by-additive effects for GCA and dominance-related effects for SCA and MPH, and additive-by-dominant effect for MPH was partly identified as additive effect; 2) the ranking of factors affecting heterosis was dominance > dominance-by-dominance > over-dominance > complete dominance; and 3) increasing the proportion of F₁ hybrids in the population could significantly increase the power to detect dominance-related effects, and slightly reduce the power to detect additive and additive-by-additive effects. Analyses of cotton and rapeseed datasets showed that more additive-by-additive QTL were detected from GCA than from trait phenotype, and fewer QTL were from MPH than from other dependent variables.

Interacted QTL mapping in partial NCII design provides evidences for breeding by design

The utilization of heterosis in rice, maize and rapeseed has revolutionized crop production. Although elite hybrid cultivars are mainly derived from the F₁ crosses between two groups of parents, named NCII mating design, little has been known about the methodology of how interacted effects influence quantitative trait performance in the population. To bridge genetic analysis with hybrid breeding, here we integrated an interacted QTL mapping approach with breeding by design in partial NCII mating design. All the potential main and interacted effects were included in one full model. If the number of the effects is huge, bulked segregant analysis were used to test which effects were associated with the trait. All the selected effects were further shrunk by empirical Bayesian, so significant effects could be identified. A series of Monte Carlo simulations was performed to validate the new method. Furthermore, all the significant effects were used to calculate genotypic values of all the missing F₁ hybrids, and all these F₁ phenotypic or genotypic values were used to predict elite parents and parental combinations. Finally, the new method was adopted to dissect the genetic foundation of oil content in 441 rapeseed parents and 284 F₁ hybrids. As a result, 8 main-effect QTL and 37 interacted QTL were found and used to predict 10 elite restorer lines, 10 elite sterile lines and 10 elite parental crosses. Similar results across various methods and in previous studies and a high correlation coefficient (0.76) between the predicted and observed phenotypes validated the proposed method in this study.