Half-sib family selection for forage yield in orchardgrass

Genetic variation for forage yield of orchardgrass is abundant, but there are few reports of progress from selection for increased forage yield. The objective of this study was to estimate direct effects of selection from one cycle of half‐sib family selection for forage yield in orchardgrass. Eleven selected populations were compared with their parent populations within three maturity groups. Populations were evaluated under hay management at three locations and management‐intensive rotational grazing at two locations. Nine of the 11 selected populations differed, by an average of 7.4%, from their parent population in forage yield. Nine of the selected populations also showed changes in Drechslera leafspot reaction, all indicating a negative genetic correlation with forage yield. Selection for high forage yield tended to result in greater ground cover and later relative maturity. However, changes in net herbage accumulation (NHA) under rotational grazing were generally not significant and were uncorrelated with changes in forage yield, indicating that forage yield of hay plots is not correlated with the NHA of grazed plots. Although genetic gains in forage yield measured under hay management were very favourable relative to other reports from the literature, the lack of correlated progress under grazing management indicates that directed selection for NHA of orchardgrass should be conducted under grazing management.     

Genetic divergence in two tropical maize composites after four cycles of reciprocal recurrent selection

Two tropical maize composites were subjected to four cycles of reciprocal recurrent selection to develop divergent inbred lines with good combining ability. This study was conducted to examine the extent of genetic diversity, changes in allele composition and genetic structure, of 100 randomly selected S₁ lines each from the original (C₀) and advanced (C₄) selection cycles of TZL COMP3 and TZL COMP4, genotyped using single nucleotide polymorphism (SNP) markers. Results revealed that the proportion of alleles at both low and high frequencies decreased from C₀ to C₄, whereas those at intermediate frequencies increased at C₄ in the two composites. More unique and other alleles were lost at C₄ in TZL COMP3 relative to those in TZL COMP4. The changes in different measures of genetic diversity were either small or negligible with selection in the two composites. The proportion of markers departing from Hardy–Weinberg equilibrium (HWE) decreased with selection, whereas the total number of pairs of markers in linkage disequilibrium increased with selection in the two composites. Examination of changes in population structures using a model‐based approach as well as cluster and multivariate analyses found a high degree of concordance in stratifying the 400 S₁ lines into four non‐overlapping groups corresponding to the two selection cycles each within the reciprocal composites. The observed molecular‐based divergence between cycles within the same composite and the clear differentiation between the complementary composites highlight the importance of reciprocal recurrent selection for preserving genetic diversity for long‐term selection. This increases the potential of the advanced selection cycles to sustain genetic gain in productivity of hybrids adapted to the savannas in West and Central Africa.     

Recurrent phenotypic selection for forage yield in rye

Summary Cultivars of Cucurbita pepo and other Cucurbita species were characterized by RFLP analysis using different fragments of the ribosomal intergenic spacer (IGS) of Cucurbita pepo as hybridization probes. Several cultivars could be distinguished by a specific rDNA restriction pattern, whereas some cultivars showed an identical RFLP pattern suggesting a closer relationship. Other species of the genus Cucurbita exhibited strong cross-reaction with the C. pepo spacer probes, in contrast to DNA of Cucumis species which did not cross-hybridize.Abbreviations IGS intergenic spacer - ITS internal transcribed spacer - kbp kilo base pairs - rDNA ribosomal DNA - RFLP restriction fragment length polymorphism - rRNA ribosomal RNA     

The development of specific SNP markers for chromosome 14 in cotton using next‐generation sequencing

Lacking of reference genome sequence for the development of stable molecular markers for specific chromosomes (intervals) remains to be a challenge in cotton, which was a necessary step in fine mapping of gene (QTL). In this study, the feasibility of development of single‐nucleotide polymorphism (SNP) markers between CS‐B14Sh (a substitution line for short arm of Chromosome 14) and TM‐1 (the recurrent parent) was explored using next‐generation sequencing (NGS) based on reduced representation libraries (RRLs). High‐quality genome sequences, representing about 7.1%, 8.8% and 10.4% of the tetraploid cotton genome, were generated for TM‐1, 3‐79 (the donor parent) and CS‐B14Sh, respectively. A total of 397 putative SNP markers were detected between CS‐B14Sh and TM‐1, and most (358) of them were also detected between TM‐1 and 3‐79. Allele‐specific PCR method was used for validation of 40 SNP markers, and 27 of them showed polymorphism between TM‐1 and CS‐B14Sh, and a linkage group comprising of 25 SNP markers and five SSR markers was constructed. The order of SNP markers agreed well with the position of them on Chr05 of D genome, which further approved the truth of SNPs detected. The results suggested that the development of SNP markers in specific genome region using NGS was efficient in substitution or near‐isogenic lines.     

QTL mapping of BNYVV resistance from the WB258 source in sugar beet

Rhizomania, caused by Beet necrotic yellow vein virus (BNYVV), is an important sugar‐beet disease worldwide. The aim of this study was to investigate and map BNYVV resistance from the WB258 source. Presence of a major resistance gene (termed Rz5) was indicated by ～1 : 1 segregation of virus levels in a population of 170 individuals derived from WB258. The maximum logarithm of odds (LOD) position for Rz5, identified by interval mapping, explained ～81% of the phenotypic variance. Rz5 was mapped alongside the previously identified Rz4 from the R36 source. Rz4 and Rz5 were located to 6.9 cM and 6.0 cM regions, respectively, on chromosome III by interval mapping. These locations corresponded well to the position of the widely deployed Rz1 gene, suggesting that the three genes could represent an allelic series. Physical mapping is probably required to confirm this however. BNYVV resistance genes from novel sources are potentially important in breeding for more durable resistance either as separate genes or as BNYVV race‐specific alleles.     

Identification of novel QTL for leaf traits in soybean

Several leaf traits of soybean (Glycine max L. Merr.), including leaf area (LA), leaf shape (LS) and specific leaf weight (SLW) may be related to soybean yield. The objective of this study was to identify novel quantitative trait loci (QTL) for LA, LS and SLW in a recombinant inbred line (RIL) population. The phenotype data were collected in 2011 and 2012 for 93 F_7:10 RILs using a randomized complete block design with 2 replicates each year. Five hundred and sixteen single‐nucleotide polymorphism (SNP) markers and the phenotype data were used to detect QTL using single marker analysis (SMA) and composite interval mapping (CIM). Single markers analysis identified 26 QTL for the three traits, of which 17 were novel and the rests were previously reported QTL. Most of these QTL were also identified by CIM. Most QTL reported in this study were in close proximity (<1 cM) of one or more SNP markers. These publicly available SNP markers with close linkage to LA, LS and SLW should be useful for marker‐assisted breeding for these traits.     

Quantitative trait locus analysis for soybean (Glycine max) seed protein and oil concentrations using selected breeding populations

Soybean seed protein and oil concentrations are important traits that directly affect the quality of soyfoods. Many studies and breeding programmes have been conducted to find major quantitative trait loci (QTL) that regulate protein and oil concentrations and to develop soybean cultivars with high protein and/or oil content. The purpose of this study was to identify these QTL using a selected breeding population. The population was tested in field conditions over a period of 3 years. Seed protein and oil concentrations were measured each year. Single‐nucleotide polymorphisms (SNPs) were used to construct genetic map using a 180K SoyaSNP array, which identified 1,570 SNPs. We identified 12 QTL for seed protein, 11 for seed oil concentration and four for both traits. Among these, 17 QTL were closely mapped to previously reported QTL, whereas ten sites were novel. Several QTL were detected across at least two experimental years. These loci are good candidate QTL for optimal seed protein and oil concentrations. Our results demonstrate that favourable target QTL can be successfully identified using selected breeding populations.     

Independent target region amplification polymorphism and single‐nucleotide polymorphism marker utility in genetic evaluation of sugarcane genotypes

The independent target region amplification polymorphism (TRAP) and single‐nucleotide polymorphism (SNP) marker s were used for genetic evaluation of different selected 47 sugarcane genotypes. A total of 23 pairs of TRAP markers generated 925 alleles, of which 74% alleles were polymorphic. Polymorphism was generally high (>50%), ranging from 54 to 98%. The polymorphism information content (PIC) values 0.20 varied among the primer combination ranging from 0.17 in SAI + Arbi 2 to 0.31 in GL 2+ Arbi 1 with an average of 0.24. However, the Pearson correlation between PIC and power of discrimination (PD) was found to be less significant. Single‐nucleotide polymorphisms were used first time for the assessment of genetic diversity among different species of Saccharum and cultivated sugarcane varieties. The SNPs were detected from 454 sequencing. A total of 245 SNP markers were assayed across the 47 genotypes, and 167 SNPs were found to be polymorphic. The PIC values ranged from 0.04 to 0.38 with an average of 0.21, and their respective PD varied from 0.58 to 0.04 with an average value of 0.31. The obtained results relatively significant were compared with the other marker systems through genetic similarity and the clusters formed in different unweighted pair group method with arithmetic mean clustering dendrogram. The clustering analysis established genetic relationship in the order of Erianthus > Sclerostachya > Narenga > Saccharum spontaneum > S. robustum > S. barberi > S. officinarum/cultivars. These results ratify TRAP and SNP marker systems for assessing genetic diversity studies, and more diversified Erianthus spp. can contribute substantially towards sugarcane varietal improvement through breeding with Saccharum spp. or hybrid cultivars.     

A comparison between single plant plots and five plant plots for the initial selection stage of a potato breeding programme

Summary The efficiency of single plant selection in the initial selection stage of a potato breeding programme was examined. A random sample of potato clones was grown in single plant plots and also in tworeplicates of five plant plots. After harvest, each plot was visually assessed by three potato breeders; total tuber weight and number of tubers per plant were also recorded, from which mean tuber weight was calculated. The error variances of the single plant plots were found to be significantly greater than from the five plant plots for total tuber weight, mean tuber weight and number of tubers per plant, but not significantly different for breeders' preference. Coefficients of correlation between single and five plants plots were significantly greater than zero for all traits examined, but they were lower than the corresponding correlations between the two replicates of five plant plots. Although a random sample of clones was examined, each clone had been assessed for breeders' preference the previous year. When the clones were grouped according to the previous years preference scores, it was found that the correlation coefficients between single and five plant plots for breeders' preference were inversely related, in magnitude, to the mean preference score of each group. It was concluded that single plant selection was generally ineffective, particularly when only the better clones, from the previous years assessment, are examined.     

Genomewide association analysis of salt tolerance in soybean [Glycine max (L.) Merr.]

Salinity is a common abiotic stress causing soybean [Glycine max (L.) Merr.] yield loss worldwide. The use of tolerant cultivars is an effective and economic approach to coping with this stress. Towards this, research is needed to identify salt‐tolerant germplasm and better understand the genetic and molecular basis of salt tolerance in soybean. The objectives of this study were to identify salt‐tolerant genotypes, to search for single‐nucleotide polymorphisms (SNPs) and QTLs associated with salt tolerance. A total of 192 diverse soybean lines and cultivars were screened for salt tolerance in the glasshouse based on visual leaf scorch scores after 15–18 days of 120 mM NaCl stress. These genotypes were further genotyped using the SoySNP50K iSelect BeadChip. Genomewide association mapping showed that 62 SNP markers representing six genomic regions on chromosomes (Chr.) 2, 3, 5, 6, 8 and 18, respectively, were significantly associated with salt tolerance (p < 0.001). A total of 52 SNP markers on Chr. 3 are mapped at or near the major salt tolerance QTL previously identified in S‐100 (Lee et al., 2014). Three SNPs on Chr. 18 map near the salt tolerance QTL previously identified in Nannong1138‐2 (Chen, Cui, Fu, Gai, & Yu, 2008). The other significant SNPs represent four putative minor QTLs for salt tolerance, newly identified in this study. The results above lay the foundation for fine mapping, cloning and molecular breeding for soybean salt tolerance.     

Genome‐wide association mapping and candidate gene analysis for saturated fatty acid content in soybean seed

Saturated fatty acids (FA), an important component of soybean oil, plays a crucial role in the nutritional value of soybean oil through different concentration and relative proportions. In this study, an association population of 185 diverse soybean accessions was used to identify quantitative trait nucleotide (QTN) and scan candidate genes via genome‐wide association analysis (GWAS), which was based on high throughout single‐nucleotide polymorphisms (SNPs) developed via the Specific Locus Amplified Fragment Sequencing (SLAF‐seq) approach. A total of 33,149 SNPs were identified with minor allele frequencies (MAF) >4%, which covered 97% of the soybean whole genome. For the two saturated FA concentration, including palmitic acid (PA) and stearic acid (SA), up to 65 SNPs were verified via GWAS. Among them, 35 and 16 SNPs loci were the novel loci for PA and SA, respectively. There were other six loci for PA and eight loci for SA overlapped or located in the linked genomic regions reported by the previous study. Furthermore, many loci were repeated in more than two environments, and four pair of pleiotropic loci (PA‐3‐2 and SA‐3‐2, PA‐11‐2 and SA‐11‐1, PA‐12‐2 and SA‐12‐1, and PA‐17‐1 and SA‐17‐2) had similar genomic regions, which might control both PA and SA simultaneously. A total of 49 genes, which could participate in lipid biosynthesis pathway or hormone metabolism, were identified as the potential candidate genes associated with saturated FA. The identified loci with beneficial alleles and the candidate genes would be valuable for studying the molecular mechanisms of saturated FA and further for improving nutritional value of soybean oil.     

Identification and confirmation of quantitative trait loci for stachyose content in soybean seed

Stachyose is an unfavorable sugar in soybean meal that causes flatulence for non‐ruminant animals. Understanding the genetic control of stachyose in soybean will facilitate the modification of stachyose content at the molecular level. The objective of this study was to identify quantitative trait loci (QTL) associated with seed stachyose content using simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers. A normal stachyose cultivar, ‘Osage’, was crossed with a low stachyose line, V99‐5089, to develop a QTL mapping population. Two parents were screened with 33 SSR and 37 SNP markers randomly distributed on chromosome 10, and 20 SSR and 19 SNP markers surrounding a previously reported stachyose QTL region on chromosome 11. Of these, 5 SSR and 16 SNP markers were used to screen the F_3:4 lines derived from ‘Osage’ x V99‐5089. Seed samples from F_3:5 and F_3:6 lines were analyzed for stachyose content using high‐performance liquid chromatography (HPLC). Composite interval mapping analysis indicated that two stachyose QTL were mapped to chromosome 10 and 11, explaining 11% and 79% of phenotypic variation for stachyose content, respectively. The SSR/SNP markers linked to stachyose QTL could be used in breeding soybean lines with desired stachyose contents. Chi‐square tests further indicated that these two QTL probably represent two independent genes for stachyose content. Therefore, a major QTL was confirmed on chromosome 11 and a novel QTL was found on chromosome 10 for stachyose content.     

Development of a kompetitive allele‐specific PCR marker for selection of the mutated Wx‐D1d allele in wheat breeding

Waxy (Wx) protein is a key enzyme for synthesis of amylose in endosperm. Amylose content in wheat grain influences the quality of end‐use products. Seven alleles have been described at the Wx‐D1 locus, but only two of them (Wx‐D1b, Wx‐D1e) were genotyped with codominant markers. The waxy wheat line K107Wx1 developed by treating ‘Kanto 107’ seeds with ethyl methanesulphonate carries the Wx‐D1d allele. However, no molecular basis supports this nomenclature. In the present study, DNA sequence analysis confirmed that a single nucleotide polymorphism in the sixth exon of Wx‐D1 changed tryptophan at position 301 into a termination codon. Based on this sequence variation, a PCR‐based KASP marker was developed to detect this point mutation using 68 BC₈F₁ plants and 297 BC₈F₂ lines derived from the cross ‘Ningmai 14’*9/K107Wx1. Combined with codominant markers for the Wx‐A1 and Wx‐B1 alleles, waxy and non‐waxy near‐isogenic lines were distinguished. The KASP marker was efficient in identifying the mutant allele and can be used to transfer waxiness to elite lines.     

Family selection in plant breeding

Summary Plant breeding programmes rarely take explicit practical account of the two sources of genetic variance, namely between and within full-sib families, even though existence of these two sources of variation has long been recognised. This paper refers to inbred and clonal crops, not to outbred, seed-propagated species. Theory suggests that the two variances should be of similar size, sometimes very similar. Good comparisons have never been made because variance within families is laborious to estimate. It is proposed that sets of families be assayed as to means in formal trials and only the best few, judged against standards as having potential for superior segregates, should be exploited thoroughly. The calculation as to approximate equality of genetic variances between and within families is important. The vast majority of families should probably be discarded without further ado, and at considerable economy. Sensible decision-making requires an economic component in order to exploit the trade-off between the cost of the initial trial and families discarded without further cost. The object of this paper is a critical review of practical principles, not a general review of a large and diffuse literature.     

Analysis of Duplicate Genes in Soybean

Gene duplication is a major determinant of the size and gene complement of eukaryotic genomes （Lockton and Gaut, 2005）. There are a number of different ways in which duplicate genes can arise （Sankoff, 2001）, but the most spectacular method of gene duplication may be whole genome duplication via polyploidization. Polyploidy has long been accepted as an important and recurring feature of genome evolution （Wendel, 2000）. The long-term evolution of polyploidy genomes is often followed by a diploidization process occurring through an extensive genome rearrangements both at the gene and chromosome levels （Wolfe, 2001）.     

Development of a core set of KASP markers for assaying genetic diversity in Brassica rapa subsp. chinensis Makino

Single‐nucleotide polymorphisms (SNPs) are rapid, economical and reliable genotyping tools. Non‐heading Chinese cabbage (Brassica rapa L. subsp. chinensis Makino) is now an economically important vegetable crop worldwide. In this study, 1,167 SNPs were evaluated for 7polymorphism among 70 representative non‐heading Chinese cabbage inbred lines using a Kompetitive Allele Specific PCR (KASP) genotyping assay. On the basis of identified polymorphisms and the results of a principal component analysis, we selected 50 core SNPs that were balanced sufficiently to provide adequate information for genetic identification. The core SNPs were used for construction of a neighbour‐joining dendrogram that separated the 70 inbred lines into four main groups and several subgroups corresponding to Caixin, Heiyebaicai, Huangxinwu, Naibaicai, Taitsai, Pak‐choi, and Wutatsai. This categorization was superior to that achieved using a dataset of 479 polymorphic SNPs. To confirm the utility of the core SNP markers in genetic identification, we tested their stability and resolution using 162 commercial hybrid cultivars. The SNPs, which represent a cost‐effective, accurate marker set for germplasm analysis and cultivar identification, are suitable for molecular marker‐assisted breeding in non‐heading Chinese cabbage.