Molecular diversity of Egyptian cotton (<Emphasis Type="Italic">Gossypium barbadense</Emphasis> L.) and its relation to varietal development

Twenty-eight Egyptian cotton (Gossypium barbadense L.) genotypes (varieties and hybrids) were used for analysis of genetic diversity using DNA based markers (ISSR, SSR, and EST) and to study varietal development of cotton. The ISSR markers gave the highest percentage of polymorphic bands as well as polymorphic information content compared with the other molecular markers (i.e. EST and SSR markers). Using clustering analysis, no general clustering according to the pedigree history of the genotypes was observed. Using principal coordinate analysis (PCOORDA), cotton genotypes were separated by the first three principal coordinates (PC1, PC2, and PC3) accounting for 11.5, 8.6, and 7.2% of the total genetic variance, respectively. The cotton genotypes were distributed into three parts based on the first PC, each part containing a group of varieties having a common ancestor. ‘Giza 12’ variety was the common ancestor for the varieties included in the first part and ‘Ashmouni’ variety was the common ancestor for the varieties included in the second part, while both ‘Sakha 3’ and ‘Sakha 4’ varieties were common ancestors for the varieties included in the third part. The results of the PCOORDA also showed better resolution of the genetic diversity than cluster analysis especially in the illustration of the varietal development of cotton. That means that principal coordinate analysis can be strongly used either alone or in combination with cluster analysis to discuss both genetic diversity and varietal development in the cotton genotypes.     

Breeding potential of inbred lines derived from five maize (<Emphasis Type="Italic">Zea mays</Emphasis> L.) populations

This review on the resistance to wheat blast disease focus on the latest knowledge useful for the breeders, but also takes into account the lacks in these knowledge. To tackle this disease, it is relevant to apply a breeding strategy which has previously proven its efficacy for obtaining rice varieties with a high level of partial and durable resistance to blast. But, incomplete information is available on wheat blast resistance. Therefore, firstly, it is necessary to adjust this breeding strategy considering the worst hypothesis corresponding to every lack of knowledge. Next, the possible invalidation of every hypothesis can allow simplifying the breeding schema and its implementation. For every lack of knowledge, the practical consequences of the corresponding worst hypothesis, the study of its validity and the consequences of its possible invalidation are explained. Scientific arguments, materials and methods details are provided with the latest available references.     

Capturing genetic variability and selection of traits for heat tolerance in a chickpea recombinant inbred line (RIL) population under field conditions

Chickpea is the most important pulse crop globally after dry beans. Climate change and increased cropping intensity are forcing chickpea cultivation to relatively higher temperature environments. To assess the genetic variability and identify heat responsive traits, a set of 296 F_8–9 recombinant inbred lines (RILs) of the cross ICC 4567 (heat sensitive) × ICC 15614 (heat tolerant) was evaluated under field conditions at ICRISAT, Patancheru, India. The experiment was conducted in an alpha lattice design with three replications during the summer seasons of 2013 and 2014 (heat stress environments, average temperature 35 °C and above), and post-rainy season of 2013 (non-stress environment, max. temperature below 30 °C). A two-fold variation for number of filled pods (FPod), total number of seeds (TS), harvest index (HI), percent pod setting (%PodSet) and grain yield (GY) was observed in the RILs under stress environments compared to non-stress environment. A yield penalty ranging from 22.26% (summer 2013) to 33.30% (summer 2014) was recorded in stress environments. Seed mass measured as 100-seed weight (HSW) was the least affected (6 and 7% reduction) trait, while %PodSet was the most affected (45.86 and 44.31% reduction) trait by high temperatures. Mixed model analysis of variance revealed a high genotypic coefficient of variation (GCV) (23.29–30.22%), phenotypic coefficient of variation (PCV) (25.69–32.44%) along with high heritability (80.89–86.89%) for FPod, TS, %PodSet and GY across the heat stress environments. Correlation studies (r = 0.61–0.97) and principal component analysis (PCA) revealed a strong positive association among the traits GY, FPod, VS and %PodSet under stress environments. Path analysis results showed that TS was the major direct and FPod was the major indirect contributors to GY under heat stress environments. Therefore, the traits that are good indicators of high grain yield under heat stress can be used in indirect selection for developing heat tolerant chickpea cultivars. Moreover, the presence of large genetic variation for heat tolerance in the population may provide an opportunity to use the RILs in future-heat tolerance breeding programme in chickpea.     

A new gene <Emphasis Type="Italic">Bph33</Emphasis>(<Emphasis Type="Italic">t</Emphasis>) conferring resistance to brown planthopper (BPH), <Emphasis Type="Italic">Nilaparvata lugens</Emphasis> (Stål) in rice line RP2068-18-3-5

The rice brown planthopper (BPH) Nilaparvata lugens (Stål) is one of the major pests of rice across Asia. Host-plant resistance is the most ecologically acceptable means to manage this pest. A rice breeding line RP2068-18-3-5 (RP2068) derived from the land race Velluthacheera is reported to be resistant to BPH populations across India. We identified a new R gene [Bph33(t)] in this line using advanced generation RILs derived from TN1 × RP2068 cross through phenotyping at two locations and linkage analysis with 99 polymorphic SSR markers. QTL analysis through IciMapping identified at least two major QTL on chromosome 1 influencing seedling damage score in seed box screening, honey dew excretion by adults and nymphal survival. Since no BPH R gene has been reported on chromosome 1, we designate this locus as a new gene Bph33(t) which accounted for over 20% of phenotypic variance. Scanning the region for candidate gene suggested two likely candidates a leucine rich repeat (LRR) gene and a heat shock protein (HSP) coding gene. Expression profiling of the two genes in the two contrasting parents and RILs showed induction of the HSP gene (LOC_Os01g42190.1) at 6 h after infestation while LRR gene did not show such induction. It is likely that the HSP represented Bph33(t).     

Effectiveness of early-generation testing applied to upland rice breeding

A plant breeding program is a long-term investment. Therefore, periodic assessment of the effectiveness of a breeding strategy is essential to maximize genetic gains per unit of time and resource invested. In this work, we assessed the effectiveness of the early-generation testing (EGT) approach used in the upland rice (Oryza sativa L.) breeding program at Embrapa (Brazilian Agricultural Research Corporation), Brazil, estimating the genetic progress achieved for three traits in two distinct phases, spanning 15 years. In the first phase (from 2003 to 2010), it was used the bulk method within F₃ progenies with prior testing of F₂ crosses, while in the second phase (from 2010 to 2017), it was used the bulk method within F₂ progenies. The dataset comprised 70 yield trials, involving 1884 F_3:5 progenies (phase I) and 925 F_2:4 progenies (phase II) from an elite population, and 10 check cultivars, evaluated for grain yield (GY), plant height (PH) and days to flowering (DTF). For estimating the genetic gain, we adapted a generalized linear regression method to compute bi-segmented linear regression coefficients. Desirable genetic gains were achieved only for GY in both phases of the breeding program, with 78.75 kg ha^?1 year^?1 (2.68%) in the first phase, and 53.78 kg ha^?1 year^?1 (1.54%) in the second phase. These results show the effectiveness of EGT, especially via bulk method within F₃ progenies with prior testing of F₂ crosses, applied to upland rice breeding. Some refinements are discussed in the method to make it more cost-effective and more efficient in achieving genetic gains.     

Study on the relationship between genetic variation of DNA methylation and heterosis in soybean leaves

In order to well understand the molecular basis of heterosis in soybean, the methylation-sensitive amplification polymorphism (MSAP) method based on capillary electrophoresis was used to estimate levels and patterns of cytosine methylation in 15-day post-emergence leaves of four parental lines [Jilin 47 (no. 19), EXP (no. 12), Jilin 38 (no. 3) and Yi 3 (no. 6)] and 12 hybrids [Jilin 38 × Yi 3(3 × ?6), Jilin 38 × ?EXP(3 × ?12), Jilin 38 × ?Jilin 47(3 × ?19), Yi 3 × ?Jilin 38(6 × ?3), Yi 3 × ?EXP(6 × ?12), Yi 3 × ?Jilin 47(6 × ?19), EXP × Jilin 38(12 ×?3), EXP × Yi 3(12 × ?6), EXP × ?Jilin 47(12 × ?19), Jilin 47 × ?Jilin 38(19 × ?3), Jilin 47 × Yi 3(19 × 6), Jilin 47 × EXP(19 × 12)]. In addition, 12 traits of the hybrids and their parents were also analyzed to understand the relationship between DNA methylation variation and heterosis. MSAP results showed that the total relative methylation level of all hybrids was lower than the corresponding middle parent value, indicating that the methylation degree was decreasing. And may express a variety of genes related to the phenotypic variation of hybridization. Moreover, the hemi-methylation levels of Jilin 38 × Jilin 47 and Yi 3 × Jilin 47 hybrids and full-methylation levels of EXP × Yi 3 and EXP × Jilin 47 hybrids was significant higher than the corresponding mid-parent values. In addition, the heredity of methylation from parents in hybrids is more than the variations, in which there were four types appeared great higher: A1, B4, B8, and D2. Furthermore, the results of relationship between genetic variation in DNA methylation and heterosis showed that the hypo-methylation had a promoting effect to increase node number, and the hype-methylation of hybrids was helpful to add to stem thick. Our results may provide new insights into well understanding the molecular mechanisms of heterosis at the epigenetic level in soybean.     

Signatures of divergent selection for cold tolerance in maize

Divergently selected genotypes can be used for detecting the genomic regions affecting the selected trait (selection signature). Moreover, the genetic distances (GDs) among divergently selected lines can be correlated with the agronomic performances of the crosses among them. Using as source the maize F₂ of B73?×?IABO78, we previously conducted four cycles of divergent recurrent selection and three cycles of divergent selection in inbreeding for cold tolerance at germination. We finally obtained 10 lines selected for low (L) and 10 lines selected for high (H) cold tolerance, which exhibited a notable divergence for both the selected and associated traits. Herein, we investigated the 20 lines and the 28 single diallel crosses among eight random lines (four L and four H); the main objectives were to identify the putative regions controlling the selected and associated traits and to study the relationships between crosses performances and GDs among their parental lines. Allele frequencies at 932 recombination blocks based on 19,220 polymorphic SNPs were obtained for the two lines’ groups; the F _ST calculated across sliding windows indicated 18 regions highly divergent between groups. The increasing alleles for cold tolerance were contributed by both parents, consistently with the transgressive segregations previously found. Several regions associated to DG also affected various agronomic traits. The cross performances showed some relationships with the genetic distances among parental lines for traits affected by dominance, provided that all crosses were considered, while these relationships vanished when only L?×?H crosses were examined.     

Identification of superior parents and hybrids for improving canola production under optimum and late sowing conditions

Major advancement in canola breeding depends on heterotic hybrids that require high general combining ability (GCA) and specific combining ability (SCA) inbred lines. In order to estimate heritability, gene action type, GCA, SCA and heterosis and to identify superior hybrids with wider adaptation to cold, one hundred canola hybrids were produced by crossing 10 lines and 10 testers in a Line?×?Tester mating design. The F₁ and F₂ generations were sown in α-lattice design in 2012 and 2013 growing seasons under optimum (early October) and late sowing (early November) conditions to be evaluated for days to flowering, days to physiological maturity, number of pods per plant, number of seeds per pod, thousand seed weight, seed yield and leaf electrical conductivity. The combined analysis indicated sufficient genetic diversity in the population and significant difference between two sowing date. The Line?×?Tester analysis presented significant GCA and SCA effects for all studied traits across optimum and late sowing conditions. The main gene action type was found to be non-additive, especially incomplete dominance and over-dominance in both conditions. Narrow-sense heritability ranged from low to moderate whereas broad-sense heritability was recorded more than 60% for all of the studied traits in both generations and conditions. The average heterosis in F₂ population for all studied traits was lower than that in F₁ representing this fact that heterosis is generally related to the heterozygosity at the population level and poorly correlated with heterozygosity at the individual level.     

Effect of maturity and temperature on breeding for mid-oleic soybean lines under the high heat conditions of the Mississippi Delta,USA

Soybean (Glycine max (L) Merr.) seed is an important source of oil for human consumption. Increasing the percentage of oleic acid in soybean seed oil is an important breeding objective because increasing the oleic acid content improves the oxidative stability of the oil. Extensive literature shows that temperature during seed-fill is positively correlated with the content of oleic acid in soybeans. In addition, it was shown that a maturity QTL was linked to an oleic acid QTL. The Mississippi Delta in the USA is a hot environment where soybean harvest begins in August, which is the hottest part of the season. The purpose of this research was to determine the possibility of developing both early- and late-maturing lines with consistent >?50% oleic acid content in Mississippi. We selected early and late segregants from three genetically different breeding populations also segregating for mid-oleic acid derived from crosses to germplasm N98-4445A, a non-transgenic freely available line with >?50% oleic acid. The selected lines were grown in 2 years in three trials at Stoneville, MS. Results indicated that no late-maturing lines (MG V) met the targeted mid-oleic acid level, whereas MG III and early MG IV lines with oleic acid over 50% were obtained. No maturity-alone effect on oleic acid content was observed, due to the bias of the strong negative correlation between maturity date and mean temperature during seed-fill. This study demonstrated that breeders can effectively develop early soybeans with oleic acid levels greater than 50% for the midsouthern USA.     

Molecular and comparative mapping for heading date and plant height in oat

Selection of oat genotypes combining earliness and short plant height could stimulate oat cultivation worldwide. However, the mechanisms involved with the genetic control of heading date and plant height traits are not fully understood to date. This study aimed to identify genomic regions controlling heading date and plant height in two hulled by naked oat populations and to compare these genomic regions with that of other grass species. Recombinant inbred lines of each population and their parents were genotyped by a 6 K BeadChip Illumina Infinium array and assessed for heading date and plant height in two sowing dates. The quantitative trait loci (QTL) affecting these traits were detected by simple interval mapping. The two oat populations showed different genetic mechanisms controlling heading date. A major QTL was identified in one of the populations, mapped into the ‘Mrg33’ consensus linkage group from the current oat map. Two other QTL were detected into the ‘Mrg02’ and ‘Mrg24’ groups, in the second population. On the other hand, both populations presented the same genomic region controlling plant height. Six SNP markers, mapping on the same linkage group within each population, were associated with the trait, regardless the sowing date, explaining more than 20% of the phenotypic variation. Five of these six markers were mapped into three different linkage groups on the oat consensus map. Genomic regions associated with heading date and plant height in oat seem to be conserved in Oryza sativa L. and Brachypodium distachyon. Our results provide valuable information for marker-assisted selection in oats, allowing selection for earliness and plant height on early segregating generations.